There are many threads with ideas and suggestions, and like them I have my own, unoriginal as they may be. I don't play the races anywhere near what would be considered equally, so rather than individual ship balance suggestions these are just general ideas and thoughts I had while playing SoaSE.
Frigates - these seem to have the most attack/defense role in the game as opposed to the support role of other classes. They are nearly universially great the way they are and these are just mostly ideas rather than personal opinions. Light and siege frigates do have their issues however.
Long Range Frigates(LRF) - maybe should have a constant damage over time effect.(Or a similar effect with quicker hits and smaller damage per hit) Each hit would be weaker but would destroy a target very quickly with the constant damage, making getting out of the way important. (This would potentially make them better against slower ships, with quick LFs being able to reach them, but the bonus damage against LF and range would keep them dead vs LRF at least in a 1 on one sense. They should probably be similar in ability to destroy slow craft so you could take one or the other for general use while one would be better against heavy cruisers and one would be better against carriers.)
LF - They seem to have trouble with their niche. Said to be good against most frigates and support cruisers, I think they should just settle on being the quick attacking infantry unit. Their problem is more that other units have been nerfed or buffed around them, disrupting their balance. By fufilling a role of being decent against most things but LRF (constant damage killing them before they close in/cause excessive damage), heavy cruisers (armor), and capital ships, and with their superior moving ability, they would keep a place as a basic unit. One consideration may be making them able to fire on a wide arc, so they could keep moving out of the forward firing arc of other ships while still attacking them. Another might just be making them turn quickly and move constantly to acheive the same flanking effect. Either of these could apply to scouts, though scouts are fine as is.
Scouts - fine as is. Maybe make them have a secondary hunt toggle function where, like explore, they move from well to well, but with hunt on, they make it a point to attack trade/refinery ships. NOTE: you can toggle explore on all selected scouts at once so I KNOW sins is capable of having all ships being affected when you activate skills, so please, PLEASE devs add the ability to scrap all/activate skills of selected ships at once.
Flak - Should possibly have a passive or active ability to weaken damage of physical (missiles, torpedos, what-have-you, possibly autocannons) ammo types in a small area around them. More importantly, there needs to be a "guard" command like in lots of other RTS that lets them stick near a single ship
Siege frigates - Lower fleet supply, lower damage, faster attack, faster speed, higher armor(not hp or shields). They should die easy without protection but should also be able to get up to a planet and do SOME damage, so they work at keeping the economy down if not taking away control of the planet. Also see artillery ships below for a different possible change.
Colony Ships - Nothing important here, but on the subject of siege frigates, I've had a pair of colony ships be able to take out a group of siege frigates attacking a planet, thus saving it. Just evidence that siege is useless as is.
Suggested craft:
Medium frigate - Something like a heavy infantry to light infantry, a destroyer type ship that could do damage to the heavier ships (like bombers compared to fighters), but more able to defend themselves than carriers. Pros: Can't be destroyed (easily) by flak or fighters. Cons: Can also be targeted by all other ships.
Artillery ship - Another type of ship that could do long range damage, but with a focus on heavy damage/aoe. Where LRF would be for quickly bringing down single ships, these would be for hitting a group of ships for heavy damage before their mitigation raised. They wouldn't be able to move while firing, however, and would fire slowly, allowing the mitigation to rise(or lower) after the first hit. [Since some LRFs can do this with an ability, I believe this should be an antimatter ability of siege frigates so they would be useful outside of one thing. They do fire equivilents to large scale nukes after all...]
Cruisers - seems like "Cruiser" means "Frigate with support role" more than "Class of ship between Frigate and Capital."
Support cruisers - They should do a little bit more damage. It does seem to be the thing that all non direct combat ships do a token amout of damage, but if these are really "Cruisers" you'd think they'd at least be a bit more powerful than non-combatant frigates in direct firing. They do have a wide variety of abilities, however, so any adjustment would have to be on a per ship basis, and thus is out of the scope of this list. The healing ones are fine since they heal things and this is more important than being able to cause damage, but the more battle oriented ones, you'd think would be battle like. If nothing else, it'd help with multiple ships targeting one thing if they did more damage to it while doing so. (If combat support frigates gained a bit more power, they'd serve the same role as medium frigates, maybe with focus on taking out other support cruisers)
Heavy cruisers - They don't feel heavy. They pop to bombers before they can act, and don't really seem to be of much use, or at least I don't use them that much, though they may have been made better recently. If the battle support cruisers are normal cruisers, then these should be second to capital ships, or rather it seems to go [[frigates with 2 guns -> heavy cruisers with 4 guns -> capital ships with 5 guns on front, 3 on each side, 2 in back, and 3 squads of strike craft]]. Even if capital ships are a bit underpowered, that's still a large jump in power. HCs should be bringing a little bit of that power to bear while caps focus more on their fleet support. That is, they should have some secondary set of weapons. (Missiles with a greater range/arc around the ship; torpedoes to hit at long range while they close in; anti strike craft guns; something like one of those or maybe just an additional gun on each side for engaging more targets.) They feel like they should be going into battle and engaging groups of lesser frigates, taking out the massed LF and flak so the carriers can swarm in. Leave the slightly-more-powerful-light-frigate to the medium frigates/attack oriented support cruisers.
Carriers - They've been nerfed way too much. The only thing with them is that they moved entirely too quickly. They should just be made to be just a bit faster than they are now but not as fast are they originally were and all other penalties removed. Being support, they should be in the back letting thier spaceplanes fight. They should be faster than most ships but not LFs, with it being on the side of making LFs even faster if need be. I don't know if strikecraft are required to be within a certain range of the carriers nowadays but that could be the way to keep them from flying everywhere if the carriers had to follow behind whenever the strikecraft got past a certain range, or with the strike craft pulling back if the carrier moves away. Mostly though, their craft die easily enough that they don't need to be reachable by anything other than light frigates or the other ships with movement altering abilities. It's also strange they don't have any abilities or upgrades (I think) Maybe while keeping their slowness, they could have an ability that lets them quickly flee to the back lines with a speed boost?
Suggested craft:
There's no higher level for anything but attack type. It'd be nice to have a flak cruiser, but I think some sort of researchable "flak pod craft" for carriers would be better.
A siege cruiser would be interesting, with a role more for invading planets. Instead of rushing in to die in an attempt to weaken the planet, these would be more durable and not easily destroyable with just hangar defenses. They wouldn't be able to bomb as fast as a comparable group of siege frigates for the same supply(more like a weak single capital bombing), but they'd be able to lock down a planet, slowing or preventing construction of ships, lowering culture/allegiance %, preventing the planet from paying taxes or collecting resources, things like that. Basically a terror ship type that puts a planet under siege in the sence that it's locked out from the outside universe, makeing it easier to take that one or preventing it assisting another world until the ships are destroyed.
Defense cruiser - They would be things like a patrol ship that could spawn a small group of fast frigate-like ships that could chase down scouts and work with the cruiser to take out other lighter ships, or a ship that could set up the missle platforms like the Sova's ability. Basically mobile ships that could deploy groups of smaller weapons platforms in needed areas. The idea being that they're mobile weapons platforms, they couldn't leave the grav well they were built in(perma jump disabled). They'd take fleet supply, being cruisers, but would serve to supplement weak areas like the edge of grav wells. There'd be more of an emphasis on their ability to contruct the temporary platforms than their own survivability in battle.
Dropships - like colony ships, but dropping marines that lower the allegance of a planet rapidly, making it go neutral, or rebel at least (spawning rebel ships). Sort of like the siege frigate of culture. Possibly could be used to restore population to an owned planet quicker. (along with more emphasis on keeping population down in the game)
Capitals - Capital ships run a line between being useful and not worth getting more than a couple of. They don't have many complaints from me; however, I feel it'd be better if non carriers had anti strike craft guns instead of hangar space, but the way things are is fine, since fighters can help take out threatening bombers. As for their abilities, they should all have 5 levels, except the special skill. (colonize would universially just allow to colonize at first level and give 4 free extracters[I think that's the max of asteroids around planets] at level 5) That's already 16 things to distribute the 10 points you get around, meaning you can't make more than one thing maxed if you want the special skill. There could also be a thing for all capital ships to raise hitpoints by %, attack and armor by %, or shields and antimatter by %, of which would also go to 5. This would push the number of things to 31 (or a more reasonable 25 if they all went to 4; 21 if the latter three were merged into 2 ), and give you versitility and reason to build more than a couple caps. If promoted to flagship, it should get another point. A side idea is that each type of cap would give a passive skill to a fleet under it if it was the leader, but that's a bit complex.
Carriers - Carrier capitals in particular should have more squads or more stike craft in general. A straight foward way is to have them have as many as their level so they end up with 10 (or 11 if they start with 2, though starting with one would be a good reason to pay to level them a couple times.) A different way would be to have their strike craft be inherently more powerful and grow in power along with the cap, before abilities (makes the most sense, why should only the cap get more powerful and not its resident pilots?)
Other ideas -
A few more ships meant to act alone/small groups might be interesting. A looter ship that acted like an npc ship and stole supplies from the opponent via raiding their trading stations/refineries(cause the planet to display negative gain for that stat), or a spy that would be thought of as a npc ship in that it wouldn't set off the alert and would drive down planetary allegance by broadcasting opposing culture. Perhaps a salvage ship that recovered a little metal for every one of your ships that died in the well within it's radius.
There should be more variance in formations, ways to make them move in spheres, walls, or spread out and surround the enemy.
Gas giants should be usable for something... not colonizable since there would be no point, but maybe something like speeding up ships in the well due to siphoning fuel/being swung around by it's gravity like they do with satellites.
Stargates - Not like the Vasari phase stabilizers, these gates would control how ships entered the grav well. That is, no matter what position they left the previous one in, they would appear from near the stargate upon entering the grav well. This could help keep things from sneaking around defenses at the cost of them appearing nearer to your planet, but at the same time could get your forces across grav wells faster. Of course phase stabilizers wouldn't be affected, assuming they somehow came to be in the same well. They could each target one phase lane (they would have to be within a certain range in of the phase lane like phase jump inhibiters, so as to keep defenses spread some), and also speed up the warping of your craft from that well to the next.( through being nearer the exit phase lane and/or due to a bonus in frendly travelling) Probably they would only apply to the TEC and Advent as some sort of reverse engineered thing. (In exchange, Vasari could get some ship that could warp in a few ships but would destroy it in the process, so they could attempt to get it to a safe place outside the gate to warp in a small fleet from a stabilizer.) Would also be something else to consider when jumping into a grav well. It would also be a tactical type, so to lessen the warping into the middle of a million guns, if nothing else.
Colonies - Logistic structures that increase the population of the planet. I thinks some starbase can do this, but there should be a logistics option like this. They'd allow allegance to go up a bit more than normal for that distance and make an attempt every so often to recolonize a bombed dead planet.(as opposed to a starbase not letting it fall out of your control, it gives the enemy a chance to take it) Mostly an idea to deal with permanent 25% outside of your own star system. Probably would also help population recover quicker and slow down drop ships.
More interplanet/stellar weapons. A phase lane gun that could fire down phase lanes and hurt incoming ships; a weapon that could fire into a system's sun and cause it to emit harmful radiation that loweres population in that system for a while; smaller interplanetary guided bombs that you set the path for and would fly through systems like a ship until it was destroyed or hit its target; a death ray that merely killed the population of a planet and kept it from growing back for a long time; a magnetic storm causing cannon that preventes strike craft launching in that well for a while; a similar cannon that cause the other effect I can't remember but prevents you from building anything, and possibly damages structures over time; a phase destabilizer that prevents warping in or out of a well at all for a while; something that shuts down devices completely; a weaker but quicker firing weapon that could send lots of periodic explosions(random and affecting whatever it hit) to a grav well(multiple ones (5+ at current superweapon slot costs) aimed at it could create a constant war zone, destroying anything built and damaging the planet, if any, on impact); a remote satellite launcher that shot out spy satellites that would let you view the grav well for the duration of it's effect.
More planet types of course, but more things to see too. Maybe giant derelicts that could be captured to collect metal from, or abandoned gigantic stations that could be colonized, burnt out worlds that are unabled to be terraformed and have no asteroids, but are capable of being bases. More than that, stars should have a chance to have random system wide effects. Maybe it emits light that makes people healthier so population grows quicker, or has unstable solar winds that weaken shields, or it's a black hole and you risk being sucked in when moving to or from it, or a double star that makes phase lane preparation and travel take longer. Things like that, but nothing too bad, given it could throw off players on multi star maps.