i think that instead of the spaceship, it should have been a superevolved creature that develops which can fly through space (so can withstand the vacuum and freezing temperature and radiation) and is part cyborg, so can have both biological weaponry and mechanical weaponry as well as wings and boosters etc with ****e-lods of customizability and evolution, just as you have with your original critters.
The thing can feed on dark matter, or hydrogen from fuel or anything crazy like that, it might be something really hard to find so you have to search out planets for it etc.
And it doesnt need to be small, this can be some huge beast, and so it can have lots of bionic parts, so you can still have all the functions of the spaceship (e.g. beaming up animals and doing genetic experiments on them).
I would prefer this SO much more than just a spaceship. I think its such a shame that the part of this game i will probably enjoy the most is going to be the stages when you have a single creature and are carrying out evolution, its a shame you pretty much lose that once you get to the tribal stage. But if they bring it back in this way in the spaceship stage, i think it has great potential.
And, with all the crazy experiemnts you are carrying out, you could be continuously looking for ways to upgrade your half machine / half creature space flying thingy either mechanically or biologically.
Any thoughts?