I'm not so sure this would work very well, even as a mod. It's much more important having well balanced sides in an RTS than in a TBS like Galactic Civ 2, especially if you're going to try and make each race unique. With custom units it would be very easy to unbalance the entire game.
I'll start my little rant off by saying this: You're absolutly right. This could and would bring tremendous balancing issues to a game such as this. Then again, the same could be said of any potential mod, unit changes or otherwise. The solution to this detrimental problem is deceptively simple. If you feel that any possible balance changes or game mechanic tweeks brought on by a player created mod could ruin your chance of having fun while playing the game with it, then don't use it.
The idea of this thread is not a matter of changing the core game for this option...that idea has already been killed (Frag for Yarlen

). This thread is simply asking the question, "Can this be done by us modders?" Me personally, I'd love to be able to take the look of the TEC and design a couple of ship hull variants as possible replacements for current models that could be swapped out as the player works their way up the tech tree. Can I do it? *Looks to Yarlin* Time will tell. And the thought of the missile barge brought up by RandomPerson...hehehe *drool*. Unbalancing? Hell yeah. Is it for everyone? Not even close.
It's not a matter of every Mod created for this game must maintain the delecate balance that was predesigned in, it's the potential of what a person can do with the engine once the mod tools come out since it's not going to be built into the game. Also what's more important, it's more ways that us, the end users, can find ways to do what playing games such as these is all about: having fun. I like playing with the stock game at first, then I start seeing ways that it could be better. That's why I mod, to enhance the amount of enjoyment I get from something that I purchased.
I don't mean to sound like I'm berating anyone with this rant, and I appoligize if that's how it is taken. I'm stating my own personal opinion.
Oh, and Kosc... *stops as Bink sees a bead of red light work it's way up towards lordkosc's head* Umm...nevermind.
Edit: And no sooner did I post this than I saw our mentor sweep in before my post with the answer to my question. There are times when I am awe struck by the power of the internet.