I've suggested before tha the roles of LF and LRF be altered, so that LF counter light and medium armoured ships, and LRF heavy and up.  This would reverse the relationship of LF to LRF, as LF would then counter LRF.  LRF would counter support, carriers and flak.

As it is LRF are too strong against too many types of ship, their minimum multiplier is 75%.  Also LRF might find it easier to get at support and carriers without being wiped out. 

The capital ships die quickly because they have no escorts- having LF as a counter to LRF would make capitals far more difficult to destroy.  I'd also switch flak to primarily anti-bombers, and make bombers the only strikecraft with decent multipliers against any type of ship.   

I'm not really a fan of dedicated scouting units. Being able to have them automatically go from place to place and drop probes is good, but the scounting itself could easily be done with any better armed ship. They're only really good for moving fast and dying (and that spam thing people were complaining about.) They do have the anti-mine role for what it's worth. Rather than elmintating them, maybe some sort of espionage ship would be created, like a ship that comes out of a phase lane still in phase space, and can sneak up to cause damage unless a scout reveals it.

Siege frigates would be anti-structure cruisers also. Also either faster or harder to damage. 

Support isn't as great as it could be, in some cases. Maybe there could be an non-stackable aura around support ships, like how some passive abilities already have ranges. In example, flak would have ships take less damage from strike craft, the TEC command cruiser would be able to increase the attack abilities just by being near the ships.

Capital ships would be strong against everything but bombers. Nothing else would do above 80% to them. That's about as much strength as they need. Really only Heavy Cruisers and Battleships would be able to hurt them in any quick way. I can't remember if it's ships or weapons that have the anti-___armor types, but the Battleships and HC would have an anti-battleship gun/ability and be the only thing to do more than 100%

It would be easier to organize fleets. You could have ships guard specific ships or have them patrol paths. You would be able to add a ship to a fleet by having it move to the fleet icon or in any other way than selecting them all and pushing the form fleet button again, assuming you didn't want auto join sending it to the wrong fleet. It would also be able to move a ship from one fleet to another.

Fighters would eat up LRF, more than they do now. They would completely stomp all over them, unless the carriers or strikecraft were being destroyed. LRF would be lighter in general and fairly easily killed. The LF > Carrier; fighters > LRF > LF though would be increased, so that they would die fairly quickly to their weakness. Ships would also die quicker in general, as they sort of take a long time to die as is.

Somehow dynamics would be changed so it's better to have small groups of ships than large waves (unless you're trying to take a planet.) Possibly so that you'd need different kinds of ships too. For instance, the gravity of planets and stars would slow down the fire rate and damage of LRF/Bombers or something, making them more effective in asteroids and the strange feature(non- star/gas giant/planer) wells.