Getting back on topic... and thinking of do-able and easier to implement changes to the combat system (not thinking a big complete redux with tons of features here)...
Bear in mind my goals: diversity of ship design and the potential for multiple valid design choices:
1) Scanners should impact tactical battles, I would have them impact the accuracy and the RANGE of a ship's weapons. Note, this is a per-ship result... a big sensor boat in the back will not help the fleet in tactical combat.
In-game justification? Jamming and false communications are too likely. Ship's rely on their own sensors when engaging... (sure why not?)
Out-game justification? Opens new combos of possibilities and creates more complication for optimizing ships and their payloads. You could be well behind in weaponry compared to your enemy, but far ahead in scanners giving you a distinct advantage in range.
2) Unused hull capacity/space = either additional ship HP or a slight increase in tactical speed, IE evasion. Lighter ships = easier to move. Not really a big deal, but I just like the idea that the 2-7 slots i couldn't fill helped somehow lol.
3) Carrier fighters that die, regenerate after three turns. Create a new hull category for Fighters that has less space and less health than tiny. Not by much mind you, but a bit. This should nerf carriers in any sort of protracted war of attrition.
4) Reduce roles to three "stances". Aggressive (moves at full speed towards the enemy), Neutral (Moves at 2/3rd's speed towards the enemy) and Defensive (Remains stationary). All targeting is simply on a "whose closest" basis...
So essentially all ships are "Capital" or "Support" with an additional "Fast" option.
5) Nerf Commanders/Admirals. They are kinda broken. In particular their speed bonuses (which with Hypergates we should need less anyhow).
6) Remove Leaders option to increase fleet HP. This is insanely broken. I can put 10 leaders on HP for an important battle, than instantly shift them back to other priorities. If there must be a fleet Leader use, have it affect strategic repair rates and reduce upgrade costs. Which you know... makes SOME SENSE.
7) Drastically reduce the size of Thrusters and make them one-per-ship.
8) Consider adding a penalty to evasion for each main drive engine you add to a ship.
That is a pretty good list, and for the most part, could be implemented via modding, so it shouldn't be drastically consuming for the developers. If I thought this was going to be a major focus for an expansion, I'd definitely come up with something more creative regarding the roles, and ideally I'd also radically change the engines into "strategic" "tactical" and "thrusters", and have various advantages and disadvantages to hull sizes in combat both in and out of orbits... so huge hulls SUCK at attacking a nest of 20 tiny hulls in orbit... but can annihilate them in open space.
Etc. etc. Lots could be done... but even a modicum of attention would make the current system more enjoyable.