[AGoetz]

Bareing in mind, that I'm still 1.2.1, I've finally had the time to get a single player game going. I didn't see specific fixes to these on your list, but I'm tired and could easily miss them :
The Tholians have a colony pod installed on all of their ships size cruiser and up - thats 300 kt of space that I presume was supposed to have been used for something else?
The Cardassins were fielding heavily armored ships, but as soon as they got shields they stopped putting armor on their designs. The new designs do actually fare better against my ships, but mine fields really rip them to pieces (a 20 unit small mine field killed 15 light cruisers)
The Feregni are the only race I'm currently in contact with that seem to be using fighters - pity the cap ships they're sending with them are very lightly armed destroyers (two pop-guns is the most offensive hardware I've seen on them yet, quite a few with storm killers, deutrium tanks and boarding parties though)
The Borg didn't expand outside of their homesystem - I conqured them fairly easily by vapourising three colony worlds and then pummeled their homeworld until they surrended.
The Klingons are showing up with Battleships that have good cloaks, but no armor or shields - they pop real easy when I've got a detector in the system.

It's year 2419.9, playing high AI, no bonus, picked all the 5k point races manually, playing federation. The Federation Sensor Array + Captain II + Starfleet Acadamy has allowed me to easily best fleets three times my size - possibly unbalanced? Just so many defensive bonuses.