Fury AI is definitely awesome.
Even under Fury AI, I still think the Myrm's a good deal, not that it certainly couldn't be better. I like the ability to carry a small pack of three Trebs or Stilletos(or even a five-pack of Rockeyes, which should be enough to kill or maim a single cruiser beam turret), yet still have 75% of my Tornado capacity, and it has enough hull strength to take collisions with Shivan fighters(and if you up the slide/reverse speeds on Shivan fighters along with Fury AI, there will be high-speed collisions in serious(gauntlet-style) furballs). Six tightly-packed Prom-S cannons give you a pretty good chance of shredding one or two head-on approaching Shivan fighters in a wave, especially backed up by Tornadoes.
I'm with the 'four guns is not enough for the Herc II' crowd. If you want to bring Maxims, you're stuck with only two of whatever else to defend yourself against shielded fighters, and that's not just enough for something that slow.
The Perseus has maneuverability over the Myrmidon. That's pretty much it; gun compatibility, missile compatibility(trade TAGs for Infyrno and Helios), missile capacity(and due to rounding, the Myrm gets an extra Treb or Stiletto), speed and afterburner performance/endurance is almost identical. If you're only chasing bombers, the Perseus doesn't give you any real advantage over the Myrm, which is why the Perseus needs to be faster(on top of all the in-game evidence(Tech Room/Command Brief) suggesting it should be); admittedly, not as fast as the Valk/Horus, but better than it is.
Boanerges is only worthwhile if well-defended and Helios are available(2/4/4 capacity). The Ursa can carry a second primary bank of Maxims for turret/subsystem work, and the Kayser turret can definitely help hurt light fighters/interceptors, especially Manticores(which I've seen it kill all by itself on occasion).
Erinyes is fine, IMO, even on Hard(you just have to be accurate), though I wouldn't be opposed to resplitting the gun banks to 6/2. 8 Prom-S sniping is too much fun to waste half your guns on Maxims(unless you're attacking a full-on cruiser fleet), and Prom-S still outranges nearly all non-beam turret guns.
The Ares is surprisingly good in handling, IMO; frankly, it handles better than the Athena(again, IMO). The difference, I think, is the Rotdamp factor. The Ares may not turn fast, but for something so supposedly heavy, it can change direction and keep a tracking shot on evading Shivan fighters pretty well(.35, whereas the Athena had the same .55 Rotdamp as all the other bombers).
My biggest problem with FS2(the main campaign, anyway) is the squadron system. Hate x ship? Too bad. Yes, it's more realistic, but hurts replayability(as opposed to FS1, where you could choose to continue to fly Apollos or Valks pretty much anywhere, if you wanted).
That, and the fact that you only get the Subach as a viable offensive primary for nearly half the game.