There are some "factual" errors in your assessment DeadZone!
The Akira class is actually older than the Galaxy Class and rather small (hence cruiser size) considering it has no real secondary hull and has a narrow saucer. And I wouldn't say the Nebula Class was a science vessel! Of course, this is little more than nitpicking.
I'm not a big fan of the AGT Enterprise, or "Galaxy-X", but I would say that it is too large for a Federation ship in the game - maybe give it 60-120kT over a regular Galaxy class to add a couple torpedoes/phasers. 1400kT is far too much!
And to be far, I'd swap the Nebula and Ambassador class sizes. The Nebula may look small - but it's just much more compacted and not really smaller.
There's also no reason why the Sovereign can't be made more advance then the Galaxy - you can easily give it another tech requirement etc. so it appears after and a simple mount for the ship to increase the firepower is not difficult at all. It's not nearly as difficult as you suggest!