And it's a very good goal.
Hi, I'm Dakroth, a member of [SF] Starfleet, one of the oldest (true) Trek fleets out there. I recently stumbled upon your mod, and as I have had the same issues with KM1.0 - namely that no one uses but five different ships, and all the other ones are absolutely worthless when up against those 5 ships - I decided to download the mod and give it a try.
First off, let me just say that I am incredibly, incredibly impressed. You have done an excellent job making all of the other races have comparably powerful ship. I am also very happy to see a properly balanced Galaxy class. (She's supposed to be a freaking battleship, yet she is almost worthless in KM1.0 unless you're up against an unskilled player!)
I hope it's not too late to make some suggestions and offer the services of myself and several other [SF] members to beta-test this properly for you. StarFleet considers Bridge Commander its 'Fleet game,' meaning that everyone in the Fleet is able to play this quality Trek based game, even though we have long since branched out and have included non-Trek games to our roster, so as to keep ourselves active and current. I don't speak for the Fleet as a whole, but I know for a fact that I and many of my comrades would love to see a well balanced version of Bridge Commander widely used.
That being said, there are a few bugs that I must point out, in the hopes we are all still paying attention. 

-First of all, there's something screwy with the multi-player. The mod works find in regards to the new ship list and the stability when multiple players are in a server, but when I try to add AI ships to the fray, they appear in a glitchy and odd sort of manner. Let me give an example: I had a friend of mine host a turkey-shoot server and throw in a couple of Federation shuttles for us to shoot at. He added several shuttles, about 5, I think, but instead of shuttles, the AIs appeared as, in one instance, an Excelsior class whos shields and health were fluctuating between 0%, 50% and 100%. These weird bug-ships also did not attack and flew sideways even though it said that they were moving at 0 kph. It took several torpedos to destroy any of them, and both my and my other friend's games crashed to desktop. The server host, however, was the only one to which the shuttles actually appeared as shuttles. The same thing happened again when we rejoined and he tried throwing in a Negh'Var.
-Second, I understand that you modified phaser damage output to be dependent on ship size, but as I was messing around with the ships in Quick Battle, I noticed that many ships' phasers appear to do absolutely no damage to shields. In most instances, I'd have to use the majority of my torpedos to get through an enemy's shields, and only then would my phasers be effective. I noticed a similar trend even with the Excalibur. It took me a considerably longer amount of time to get through a Ferengi Marauder's shields with my phasers than I would have expected with the most advanced and powerful ship in the Federation arsenal. 
-Third, and I think someone mentioned this before, I have an issue with the inaccurate phasers. I like the idea of having phasers that don't 
always hit their target, but with many ships that I've used so far, I have to be very, very close to an enemy before I could even begin to dream that my phasers would ever hit. I would suggest, if it is possible, that phaser inaccuracy be adjusted so that they are somewhat inaccurate, not totally blind. 

Other than that, I haven't seen anything else majorly problematic. If you are still up for continuing work on this project, please, let me know so I can give you a hand in testing models. My friends in Starfleet would be more than happy to test out ship models for you. And again, very, very good work so far. Keep it up.
I'll leave my contact info if you wish to contact me.
xFire: dakroth
AIM: dakroth01
Google Talk/Gmail account: Dakroth@gmail.com
Yahoo: SF_Dakroth
WIM: dakroth@live.com
(I know, I have a lot of instant messengers... I use the program Pidgin to connect to all of them (excluding xFire) at once, so if you add me, just add whichever account is the same as whatever program you use. It'll show up.)
Also, if you wish to check out [SF] Starfleet, you can find our main site at starfleets.st and our forums at starfleets.st/vb.
- [SF] Commander Dakroth