My two cents:
I think that a few smaller changes would be almost as successful in giving beam fighters some more loving.
1. Instead of base aiming speed (can't remember what it's actually called, the value for the weapon not the fire control) being "Max(ship speed, turret speed, base fire control)" it should be "Max(ship speed + turret speed, base fire control)". This change wouldn't effect the larger, slower ships too much, but it would be a huge boon to the fighters. Right now it's impossible to make a small turret to help fighters a little bit, you either have to give them a really big turret (half of which's gear is wasted) or go without.
2. I also think that we should remove the "one engine per" restriction for FACs and Fighters. I don't think that it should be based on ship size either. If you want to build a 20kton ship with 100 fighter engines then go for it.
This would require some balancing tweaks though, I already think that the enormous fuel cost of the smaller engines would make that strategy less workable than you'd think, but we'd probably want to do a couple other things to penalize it a bit further. One possibility would be to further lower small engine efficiencies, but that would harm current fighters too, as would lessening the effect of the efficiency research on small engines, or giving small engines their own separate efficiency research (that adds paperwork in general).
What I would do it increase the failure rate of the smaller engines. It should bother the existing ships too much, because they aren't high endurance craft anyways. Fighters especially spend most of their time in hangars without increasing their maintenance clock.
In addition to an all around failure rate increase, we could have a failure rate penalty for multiple engines. Say two small engines on a ship gives both of them a 20% increased failure chance, etc etc. I'd probably cap that value though, say a five-fold failure rate at ten engines or more.
Heck, if you wanted to you could also give a single exploding engine a bonus chance to spread to other engines.
That way we have the ability to make really really fast ships of all sizes, but they would be fuel-guzzling fiends that are a maintenance nightmare.