This was an idea I had several years ago for GC2. It's simple. Create a “Lab” module for starships! This Lab would produce a limited number of science points each turn, possibly bonus points for exploring anomalies, new star systems, wormholes, ext. This could be a linear progression of the survey module, or a fork in the technology tree.
I personally prefer to play a more peaceful/economically driven strategy. but I still think star ships are cool! Being a fan of Star Trek, I have always wanted to build a fleet that is not intended to be a war fleet, but could be used for defense if/when needed. If the Lab module was rather large, the ship wouldn't have room left for very many weapons. And if they cost extra maintenance, this would help balance against spam.
In GC2, I was forced to build fleets just so that my neighbors wouldn't see me as weak and attack out of some primal aggressive tendency. Even supposedly peaceful races! These fleets always wound up just sitting stagnant on top of my planets, with very board crews... While I'm not complain about this "opportunistic" mechanic, a natural solution is to give the player a reason to build a fleet that is in alignment with their civilizations values! i.e. the science vessel! Of course, with weapons for self defense