Remember the good old days when you had to choose which research paths to pursue for ships. Sure races add variety, but the game really has far less choices to make now shipwise
It would be far more interesting if you had to research a path for each ship factory class.
eg: I want a light factory that produces EMP units, a medium factory that produces cloaked vessels and a heavy factory that produces subversion ships.
Balance would be a little tougher to conceive, but I'm confident Spinner's 1337 accounting abilities could do it.
This would create a massive number of permutations of ships across the galaxy, especially considering there could be one of 4 ship "themes" to choose for each of your 3 factory classes.