I usually specialize in one weapon type, but I'm not at all sure that's the optimal way to do it in GC3.  I'm doing it that way because (1) it was the best way in GC2 and I'm stubbornly change resistant  (2) I usually have a lot more of one resource than the others and (3) I find it more convenient to research down a tech line instead of alternating among 3 tech lines.  So mostly personal preferences.

I've seen others state that it's better to mix weapon types because each weapon type on a ship can fire at independent targets, and that does seem to be a good reason.

I'm not sure I completely understand your building queue question.  Are you saying you select a factory and instead it builds a mega factory?  Do you have auto-update turned on in the govern planet window?  It might be automatically upgrading for you.  I always turn that option off as soon as I colonize a planet.

By mixing weapons I meant putting multiple weapon types (beam, missile, mass driver) on the same ship.

For more success in combat, research logistics techs so that your fleets can be bigger, and make your fleets be all escorts and capitals that you design yourself.  Put a lot of defense on the escorts with just a little offense, and then all offense and no defense on the capitals.  Make sure the designs are assigned the correct roles (escort and capital) since the ship designer often picks the wrong one.

When designing the escorts, pay attention to the weapons the enemy is using and set the defenses for that.  If you're going to be battling more than one enemy or the enemy is changing their ships, balanced across all three types is better.

It really needs to default to off.  As leaving it on is a disaster in 3.0.  Basicly it is bad 95% of the time, so why do it by default?  Much easier and safer to just turn it on when and if it is useful. 

I mean...why would you not design your own ships, and how is it not fair? Did you know that the AI cannot design its own ships? This means you can customize your ships to be better and more suited for your needs in every way compared to the AI. This is a HUGE advantage over them if I have ever seen one.

Standard ship designs always come with components that you do not really need. For example, if you only want to build a fleet of ships to defend your territory, why waste capacity on life support components or excessive engines? You can pack on weapons and shields, and let them sit on planets to defend. The AI cannot min/max like this to save cost and/or improve efficiency. The player has it good in this regard.

Also, if you want to pack more into the same capacity limit, play like me: put all of your research into reducing the mass of components and increasing capacity, build a Hyperion Shrinker (you need massive scale construction) and deck out its adjacency bonus to level 20 for a HUGE +100% to capacity to all your ship hulls. The max you can go is level 21, but that requires you to make an unjustifiable sacrifice, so just get it as high as you reasonably can. Then you can easily outdo the AI ship for ship. The only downside is that your ships will also be more expensive, but considering you can min/max your planets production, it is worth it.

You do not really need to worry too much about ship efficiency against the AI. Just put all of your latest tech on every ship you make is good enough. Upgrading preexisting ships should only be done if you really cannot afford to waste turns moving a new ship into place to replace the old ship. Otherwise, it is more cost effective for you to just decom old ships and build new ones.

To extend your ships' range, you can either equip them with more Life Support components, build a bridge of starbases, or capture planets. You can easily equip enough life support components to let your ships travel the entire map easily, though, so no need for starbases unless you are early or middle of the game on gigantic+ map sizes.

If you are not designing your own ships, then your success depends on the techs that you have researched so far because standard ships update according to your unlocked techs. Do not assume that all ships are created equal just because they are the same size. If the AI has better military tech than you, then your standards will never beat their standards unless your military tech surpasses theirs, which is unlikely since the AI has a tendency to put MUCH more effort into their war techs than they do all of the others. What can you complain about if/when you lose if you do not even try to make up for the difference by designing your own ships to maximize their effect?

How you design your ships to deal with the situation is part of the strategy. You are basically just handicapping yourself by forgoing that, and it is not even that hard to design ships. You just pick the hull size and then put on the components that you want from a list of engines, weapons, defenses, and support modules.

For example, in a free game or applicable scenario, you could pump out a bunch of crippled, glass canon ships just to keep your military rating high. These ships are never meant for actual battle unless you have no choice. They are just there to keep the AI from attacking you, so you can focus more effort into building up your colonies.

To be fair, I have not played many scenarios, but I do know that the AI almost always have some sort of advantages over the player. This is part of the challenge, and in some cases, part of the scenario (where you are supposed to be disadvantaged).

For example, if you play on higher difficulty levels, the AI will basically get cheat bonuses, like more money, production bonuses, movement bonuses, and even free tech.

This is because if the AI started out on an even playing field as the player, then the AI has no chance of winning. The AI is not smart enough to make all the decisions necessary to fully capitalize on every aspect of the game like the player can when min/maxing (and you do not even need to go that far). The AI does not know how to plan out a planet for maximum adjacency bonuses, it does not know how to effectively center starbases around as many resources as it can, and it cannot even tell when it is just sending all of its ships to the scrap heap by invading someone with massively more powerful ships.

Without some advantage over the player, everyone but the worse at strategy games can easily steamroll the AI. This applies to every strategy game out there, though.

If they are not getting bonuses from the scenario itself, then keep in mind that different races have different tech trees, which gives them access to variant techs than what you have with the race that you are playing as.

1. Population is directly tied to your raw production value. You want as much of this as possible. More production means you build things faster, get more money, more research, etc. Naturally, the more people you have, the more you can get done, right? Population is capped by the planet's class (how many tiles it has) in v3.0, so you only need enough improvements to get your population cap to this number.

2. You should specialize your planets. This is the basics to maximizing the efficiency of each planet. Outside of a few mandatory buildings, like cities and approval, most of a planet's free tiles should go toward only one type of production. Not every planet needs to have research. Pick a few planets with the best research bonuses, build a couple of factories to boost manufacturing, and then set the majority of the remaining tiles to research buildings. Do the same for financial planets. Manufacturing planets only care about having a bunch of well-placed factories. This leads to the third question....

3. Not every planet needs a shipyard. As mentioned in number 2 about specializing your planets, you only need shipyards on planets specialized in manufacturing. To take it a step further, if you can, find a cluster of 3 or more planets that are within 6-10 (max) tiles of each other, and make all of those planets into manufacturing planets. This cluster only needs 1 shipyard. This way, you can pool all of those planets' resources together to build expensive ships  much faster than you can on individual planets.

4. Generally, if you want to base your weapons and defenses on the enemies that you are fighting. If your enemy specializes in missile weapons and beam defenses, then you want to build ships with missile defenses and kinetic or missile weapons. If you have time to research, however, it is best to research all 3 defense types and have all three types on all of your ships. This is because different enemies will specialize in different weapon types most of the time, and it would be a hassle to make a specialize ship for each of your enemies. You can get away with just 1 type of weapon, however, if you are tight for time. You just need to pack on enough of it to deal decent damage. In this game, having a large fleet of glass cannons, defense-less ships with high attack power, will beat well rounded fleets any day. Who cares about defenses when you can just blow them all up before they have a chance to hit you.

5. Early on, I like to focus on capturing planets while rushing to build up get the infrastructure of my home planet, with a focus on research. Spread your Ideology around to make sure you get the Arbitration Center (Pragmatic), Intimidation Center (Malevolent), and Missionary Center (Benevolent) first. After a decent number of planets have been captured, then comes capturing resources. With version 3.0, resources have become extremely important to ensure that you have plenty of else it will bottleneck all of your development further down the line.

6. There is, but it is kind of meh. https://galciv3.gamepedia.com/Official_Galactic_Civilizations_III_Wiki

Yes, colonizing planets.

No, I had the very legitimate complaint that none of the default designs I had access to were/are as good as the AI had, even after completing a big part of the research tree.  That is something different. Succes in a 4X shouldn't be solely dependant on whether or not you use a side feature. I

If I wanted design of ships be the most important factor, I'll play Kerbal Space Program.

And if you cant contribute anything meaningfull, please don't post

Nothing wrong with you want to play with vanilla ships, but you are severely handicapping yourself by not taking advantage of the ship building feature, and indeed, it is not just a bonus add-on feature. The ships that you choose to deploy will have a massive impact on the outcome of your game.

For example, if you are trying to colonize a planet before your opponents do but you have already used up all of your colonizers, what kind of ships should you deploy? You want to get there ASAP. How are you going to do that? Does it make sense for you to build a standard colony ship with unnecessary sensors and life support? Of course not. In this case, you want to remove all of the sensors since you have already made a path to the new planet and know where it is, and if the planet is not too far away, you do not want many life support modules, if at all, either. You strip these unnecessary components, so you can add more engines to ensure you get the before your opponents.

Same thing applies to constructors. If you are trying to capture resources near home quickly, you would deploy decently fast constructors with more than one constructor module and no sensors or life support so you can quickly build starbases.

Things like this happen in real life all the time. When trying to achieve a specific goal, you would want to strip out all of the unnecessary parts and add more of the parts that really matter. For example, planes and boats get stripped of unnecessary amenities and parts all the time to accommodate their loads.

So by not maximizing the efficiency of your ships to your needs, you are not only wasting resources, you are wasting time, and speed is the life blood of battle, as they say. How you go about achieving that speed is a massive part of any strategic battle. It goes without saying the strategic importance of colonizing more planets and capturing more resources before your enemies does.

Its all even stevens in the game (on normal), your not playing the game, your playing a scenario, there are different rules because well its a scenario.....playing scenarios not the best way to learn the game, not by long shot.