Agreed. I've suggested something like this before, and probably other people have, too. Basically, if it's so much fun to do for ships, why not do it for bases, too?
Sadly, it will probably have to wait for GCIII, if then. It would be a lot to code and get the AI to use in an expansion pack. In game terms, though, I don't see why it would be terribly impractical; modules could have a BC cost, and you'd not only purchase a constructor but have to shell out BCs for construction (instead of automagically installing, say, Overlord Armor for free and with no mass or energy cost). If you wanted to add extra modules, you'd have to send out another constructor. In that respect it wouldn't be too different than the current system, the main exception being that you wouldn't have to manufacture and send out a billion contructors to get a starbase up to snuff. Influence victories wouldn't require endless streams of constructors and clicking to build essentially the exact same starbase over and over.
Heck, this might even result in a shot in the arm for milbases, too, since you could design effective bases in much the same way we do with ships. If you had the money, you could build a top of the line station.
Ah well. Fingers crossed.
