Fleet

I'm not sure what you mean by "split the fleet supply points equally between the capital ships, command ships and Titan on the one hand, and everyone else on the other".

The supply points and price should be in line with the ships power (durability, hit points, pierce, damage, speed, agility, range, abilities, etc.) so that even if you decide to go all heavy ships there is still a counterbalancing price to pay, specially since there is no upkeep resource cost per ship.

On the other hand, all these attributes should also reflect different roles of different ships within your fleet, so that light frigates and corvettes are still useful in the late game. It is my opinion that the Advent Ships achieve this perfectly and I can still find uses to Disciples and Acolytes in the late game.

If the AI is building different ships even at maximum difficulty levels then it should make for a better gameplay experience as different ships represent different threats that must be countered accordingly. The AI can only fail on increasing difficulty if it fails to use these ships as counters against their adequate targets: e.g. light frigates vs support cruisers, heavy cruisers vs corvettes/frigates, point defense vs missile ships/strikecraft, strikecraft vs corvettes/frigates/cruisers.

I like that now command ships are not available all at once. This is a step in the right direction. It is good that you can have no more than three such ships in the fleet. I would limit the number of capital ships in the fleet. Twenty would be nice.