Yeah, I stopped playing multiplayer back when you did (or a little bit before that, I got tired of fighter spams), but the game is quite a bit different now from what I understand. For one, Carrier Capitalships (yes, you heard right) are now easily the most potent in the game, in fact it seems quite common to get rushed with a pair of them. In particular, the Scinantra with scramble bombers (it got a big buff) is the favorite game abuse mechanic right now, with the Vasari in general as the most played faction now. While LRFs are indeed still powerful, in many ways bombers now share the most used unit title thanks to flak not being that effective against them and fighters still get annihilated by flak.

There is a community balance patch in the works (whose debate topics you've probably seen in the strategy forum), if you are interested in trying to make the game a lot more balanced than it is now. Otherwise, I suppose its possible we might get another patch after Stardock releases Elemental, but don't get your hopes up.

I've not got much experience with it, but the way I've been dealing with heavy amounts of bombers is not to have flak ships but rather just destroy whatever is fielding them, then the bombers eventually take care of themselves without using fighters or flak.

Yeah, Im considering quitting the game until the flak frigate is nerfed.