Hmm, having played both factions for a game or two, I've got the following:
FRAKING AWESOME. Period.
Okay, so it was awesome. To be precise:
- Klinks are VERY well balanced. The Call-To-Arms ability was very nice to see for the Neg'Vars - a ship that's otherwise well-balanced against the Sovereign gets a solid battle upgrade to make it distinctivly Klingon.
- On the other hand, Klinks are still overly dependent on Vor'Chas and D-24s. Many of the other cruisers aren't cost effective for their combat worth. That may change once attack craft are added, so I'm not worried.
- The Defiant is now a well-balanced ship vice a cheap way to destroy everything in sight (dang it, guys, was I the one who ruined this?). Good call on the Defiant balance - it's almost exactly the way I think it should be.
- Good call on the Nebula changes. I like it being approximately equivalent in firepower to the Galaxy Class, since both were peer starships. The new Gemini ability is a nice touch that makes it a worthy addition to Starfleet.
Okay, a couple gripes:
- I'm offended that there's a USS MERRIMACK in the list of Fed ship names. For god's sake, it was re-christined the VIRGINIA when it was converted to a Confederate iron-sided ship. P.S. - I recommend adding all USS IOWA (BB-61) class battleship names from WWII to the Fed Rosters. It was heavily hinted in TNG that all became GALAXY or NEBULA Class Starships (direct reference made to IOWA and MISSOURI, probably also had a WISCONSIN and NEW JERSEY).
- How is is that a Miranda Class ship has 11 supply, when an Excelsior has 13, a Steamrunner has 8, and an Intrepid 10? Make that Miranda a low-supply ship with weak attack, but very fast build. The Miranda Class hasn't killed dick since Khan took out a bunch of noobs on 1701.
- The Feds now have no cruisers. STARTREKER and I probably ruined any chance of a balanced Akira (though I would love to see it swap places with the Ambassador as a Cap Ship), but this is ridiculous. 48 support for a ship that's not quite on a par with a Vor'Cha (Vor'Cha has nearly 2X Akiras HP+SP, and does ~75% damage at only 19 support)? That leaves the Intrepid (or, per ship effeciveness, the Steamrunner) as the new Starfleet mainstay - and they clearly don't cut the mustard. Are you meaning to tell me that the Feds can't send a single class of ship up against a Vor'Cha for comparable cost? Recommendation: set the Akira supply between 24-30 (twice to 2.5X in the initial release) and make it somwhat comparable to the Vor'Cha - should keep guys like me from spamming them yet still allow for a descent Fed cruiser. Another way would be to give it more pre-requisite research so I can't build 8 weapons stations and start spamming in 10-15 minutes. The real problem with Akira spamming in the first SoA2 Entrechment release (which I am in a clear position to dictate) is that you can build 8 weapons research stations quickly, and then there are only 2 pre-requisite researches to Akiras, meaning you can spam them VERY soon.
That's my entire list of gripes. That you named a ship screwy, I want a cheap Miranda, and the Feds need a better go-to cruiser. That's an amazingly short list, guys, so pat yourselves on the back. I will be on this weekend to test out my battle theories for the new version. Don't count on me switching to play the Klinks though - I've got a couple ideas up my sleeves for how to keep the Feds as an advantageous faction - you'll just have to wait to see if my complex mathematical formulas for what strategy will win are acurate...

P.S. - If I'm being too big of a dick, let me know and I will resign myself to some grunt work for the mod. I can program tech trees, re-assign icons, and do all the craptastic work like that. I did more than a little bit of that type of work for EvilJedi and EVADERS for the Star Wars Mod, Sins of A Galactic Empire.