EDIT: Actually some of the bonus ships that come with the Ancient Shadows expansion pretty much ruin the game for me.
I see. Which ships do you refer to, out of curiosity? I've only ever played with all ship types enabled, and would be interested in re-evaluating all the common settings I've been using.
Zenith Siege Engines. I really don't like them and I think I've raged about them a couple of times before. When the AI sends 100 of them in addition to other ships you can't do shit except use a Lightning Warhead or let your Command Station be destroyed. That's because of their ability to damage everything under Force Fields (despite the force fields). So basically Zenith Siege Engines are a fleet ship version of Plasma Siege Starship.
If you want to have Ancient Shadows enabled but don't want to deal with Zenith Siege Engines you can
manually edit the .sav files to remove the unlock from the AIs as a workaround. Yes it works for AIs too. To do that you will have to go to the settings in game: ESC-->Settings-->Advanced Settings--> and enable "Don't Compress Savegames". Then open the .sav file in a text editor (I use Notepad++) and look for AI 1 and/or 2 and then for the part that starts with "04". For example "|04239:33|" means the AI has unlocked ships 239 (Lightning Frigate) and 33 (Infiltrator). If you wanted to remove the Lightning Frigate unlock you would delete "239:" so it would look like this: "|0433|" (the ":" separates different ships). Note that the AIs can reunlock these ships as long as you have hacked the appropriate backup server in-game. I guess you could make that happen by editing the .sav file too but I haven't been arsed to figure out how. Although it would be quite simple. Save before and after the hack and the compare the .sav files.
I don't remember which expansion Lightning Torpedo Frigates are from but those in addition to Spire Blade Spawners make me disable "Fast Drones" ship types. Shield bearers are also a pain in the butt not in such a bad way. They're more of a challenge rather than an annoyance. Well them protecting other ships from my Tractor beams is quite annoying but that's ok. Spire Railclusters may be a bit too powerful too but they're still ok.
So in short:
Zenith Siege Engine: A reason to disable an expansion or edit a .sav file.
Lightning Torpedo Frigate: I guess it's just that I don't like playing against these.
Spire Blade Spawners: Same as Lightning Torpedo Frigates.
Shield Bearers: May be a bit too powerful.
Spire Railclusters: Ok I guess.
As you may have noticed all low ship cap ships seem more powerful in AI's hands than in player's hands. While you can only get 24 Shield Bearers per Mark lvl the AI can get hundreds.. infinite amounts in fact.
It seems to me that low ships cap ships provide more bang for buck than high ship cap ships even if their cap stats were the same. That's because high ship cap ships aka swarmers, ultra-light and light ships have lower health so they get destroyed much faster. And every time a ship is destroyed the cap dps drops. Whereas it takes much longer for a high health (low ship cap ship) to be destroyed so they can maintain their full dps much longer. That's why Starfleet Commander and Starship Fanatic AIs are so scary.