FS1: Valkyrie
With 200 shields, the thing's a death trap, but I love flying it more than any other GTA ship. Primaries are well positioned for a Banshee/Avenger combo, the missile bank isn't great, but 120 furies is better than the Ulysses' 80 (unfortunately you are forced to choose between them and the Phoenix V, which with the Horus you aren't, but that's not that big an issue in FS1, where you can just close that additional kilometer and kill the damn thing manually). It's true successor is what I miss the most from the FS2-era arsenal; objectively the Perseus is great, but I could never love it as much.
The Athena is a work of art... and art galleries are exactly where it belongs
Attacking Shivan fighters with the Avenger is a joke. There are situations where I might find flying an Athena preferable to taking a Herc, but in the retail campaign, there are none.
As for the Hercules, the only thing better than shooting those fat bastards down is flying them
although I think you have to be a Great War veteran to actually believe that
FS2: Have I mentioned I want a Valkyrie mk II? It could hardly be worse than the Hercules mk II...
Well, it's hard not to love the sheer firepower of the Erinyes
And it's also a surprisingly versatile ship, quite apart in its dogfighting capabilities from the other heavier fighters. I also like the Ares, as a true successor to the old Hercules.
But for the situations where the Erinyes is too sluggish, the best choice is of course the Perseus.
Vasudans: In FS1, all their fighters would be very, very good if you could actually hit things with them
Well, not the Anubis, of course... the only way to make that thing at least decent is to mount the Lucifer's Shivan Super Laser on it
The Seth is the least desperate in that regard, and it also has perfectly placed secondary banks, especially when compared to the Horus's. It's actually an excellent ship for it's class, capable of engaging fighters in a quite less embarrassing manner then the Herc is.
Unfortunately, by the time of FS2, the Vasudan old arsenal doesn't stand a chance in comparison any more, and the newest additions are unimpressive. The Serapis is very lovely, but lovely isn't exactly what you want when bad, ugly things start shooting at you. But at least it can shoot and hit (!) back, which for the Vasudans is a vast improvement.
On the other hand, the Bakha and the Sekhmet are better then all the Terran bombers put together, which is strange, since it's quite different from the situation in FS1.
& an honorable mention: the best space superiority fighter in both the FS1 and the FS2 - SF Dragon
If you try flying it (armed with the GT(V)A weapons) you'll have absolutely *nothing* to complain about. Until you spend your 40 furies/80 tempests, or something touches your flimsy hull and knocks out a subsystem or two...