why do I get the most powerful ships at the beginning and have to struggle through the tech tree for middling cruisers?

Sins is certainly a very epic game that focuses more on high level strategy and less on individual tactics than most competing strategy titles. However, I think one feature that detracts from the 'epic feel' of sins is the capital ship system. This, in my mind, brings the game closer to a traditional RTS.

In the interest of early game enjoyment, fun, and extra decision making, the game grants you access to capital ships when you do not have the technology to build more than a simple frigate.

While you progress up the tech tree, you unlock new and different types of frigates, but all throughout the game the backbone of your fleet are the capital ships that the game magically grants you. The capital ships are fun to level up and specialize in their abilities (and help keep players attached to their beloved ships), but by and large they represent the military pinnacle of your civilization... and you get them at the beginning. This leaves little power to be had at the upper ends of the economic and research development paths.

In addition, the fleet crew cap system, as well as capital ships that start out weak and magically increase in ability, ensures that players will never be able to use their economic advantage to both research and develop powerful weapons of war, and after producing them in large numbers, crush the enemy. Capital ships are granted early to make the early game much more compelling, at the cost of being a mid to late game reward and tool for victory.

As well, the combat system seems designed to prolong engagements (shield mitigation, complex armor vs. weapon type balancing, light armament on most ships), when the contrary and natural desire is for combat systems to be lethal (they're designed to kill, after all!). This tends to make ships across the board (especially the deliberately weakened capital ships) feel less than satisfying.

Combined, you have freebie capital ships that do not take effort by players to earn (but do take effort to babysit), and which can't be used to overwhelmingly crush an enemy (decreased combat usefulness from what you'd expect given their size, hard fleet cap limits, requirement to first level up the ships before they become viable in combat).

This would seem to make the research trees not as compelling as they could be (you get all the cool toys at the beginning of the game), and overwhelmingly focus the game on frigate sized ships, which would seem to skew gameplay towards 'rushing'.

I haven't played any 4X games in a long time, but from what I can remember powerful tech always tends to be at the upper echelons of the tech tree, and attaining it can very well lead to victory, as these systems and technologies are designed to fight and win, not to be fun to 'play with'. Part of the fun of expanding your epic civilization is enjoying and exploiting the rewards that come from fully developing it, economically, militarily, and scientifically. By giving us the fun stuff too early, you reduce the fun we might otherwise get in the late game. I think this detracts from what would otherwise feel like a much more epic game.

Spammer would be faced with choice to keep his one Cap Ship and spam light / medium units as he does now... But other player could have 2 Cap Ships and balanced force instead which in this case would indeed counter light unit spammage

Make cap ships ignore shield mitigation, for everything.Most every cap ship maxes out the enemy mitigation after one salvo, so you will ALWAYS be doing half damage. This also means abilities like Gauss are laughably worthless since they never do anywhere close to their full damage.Problem solved.

(and I'm surprised people have been comparing them to modern navies instead of other sci-fi fleets.)

Funny. When I first showed my friend this game, he watched my Kol warp into a system, and when he saw it shoot the first pirate ship, I saw him grimmise a little, thinking it would explode. A while later, when the pirate finally poped, he said "was the small ship really strong, or was that big ship really weak?".I think Caps are fine early game, but I really wish all their stats/defences/damage went up after lvl 3. I don't know, maybe 2-3% per level or something (with no level cap). That would make late game Caps far more durable, damaging, and hopefully even scarry. . .

Why not rename the Cap ships to say "Flag Ship" or "Battleship" (I understand that there certain races have this type of ship) But thenmake another class of ship - Capital ship, where you can only have one, making it exactly like the OP stated, twice as big (visually) expensive and powerfull?