A lot of good ideas here, but I want to add a suggestion of my own.
FA is primarily a game of ship combat, and detailed rules regarding fighters and the like take away from this, bogging things down in a game that could stand to trim the fat.
To this end, the rules from the current iteration of Taskforce may be the way forward...Put the gallows away! Here me out!
For those unfamiliar, here's the rundown:
1.There are only 2 types of SRS; Interceptors and Bombers. Dice are not used to track numbers, ships have a number of tokens given on their profile along with AD/PD of those tokens. Example: Directorate Dominance Carrier has 2 Bomber tokens (AD 7) and 2 Interceptor Tokens (PD5)
2.Bombers are a weapon type able to targets ships up to 24". You declare Bomber attacks along with your other attacks, placing as many tokens as you want on as many targets as you want until you spend all tokens for that unit. When you declare to resolve Bomber attacks, roll the appropriate AD, opponent rolls PD. Once resolved, remove the tokens and place them to one side (the "Graveyard")
3.Interceptors are placed in reaction to Bomber attacks and Boarding attacks. When a friendly ship is chosen as a target of either within 24" of a vessel carrying Interceptors, you may place ONE Interceptor token on the chosen vessels base. When the attack in question is being resolved, add the interceptors PD the the targets. Once the roll is made, place the token to one side as with bombers.
4.in the End Phase, all spent tokens are returned to the appropriate ships.
(On the side, I must mention that in TF, penalties come off the number of success rolled, not the dice pools, and damage penalties from ships will also apply to SRS tokens they launch. Also, all pools are combined, no linking!)
This approach works...
1.Removes the extra fiddling around with small dice and the extra time moving tokens conventionally, speeding up play.
2.Mitigates the problems with dealing with SRS without your own.
3.Stops a lucky roll making a SRS token useless below a certain strength.
4.It lowers the PD mountain, although you would have to add the option to make Interceptors help against Torpedoes for FA, further making when to play your tokens a real choice.
Where it fails...
1. You can't make PD attacks, making Bigger Batteries useless in their current rules-The above suggestion of allowing Escorts/Bigger Batteries ad PD friendlies within Command Distance would be an effective solution, making Escorts more effective, seeing as you have to be picky with Interceptors in this system.
2. Makes current Hardpoint/Upgrade slots regarding SRS useless and in need of an effective replacement...I haven't even begun to look at that..sorry!
3. No Dogfight rules needed, again saving time.
4.Oversimplified? Assault Boats/fighter/support would have to be written back in, again adding to complexity. Suggested solutions (will replace bombers, one-for-one): Fighters- 36" AD pools lower AD than bombers;Assault Boats- AP instead of AD; Support-roll ONE extra repair Dice per Token. TESTING REQUIRED!
Sorry for another wall of text, but food for thought if nothing else,