Hi! I really enjoyed battlestation and joined in the kickstarter. I think it's a great idea to include the fans in the next project. I used to spend time developing games when I was younger and your ideas remind me so much of the sort of thing that I would have loved to work on.
The new game is looking good. I actually like the idea of clones but I think that picking the statistics of "The original" should be an important choice at the beginning. E.g. if you give him a high intelligence stat then research in the game will be quicker, a high strength may make them better in battle or make building faster, high constitution/health would improve survivabilty. Due to the clone concept this choice can then effect the whole game playthrough style and will enhance replayability.
As others say, I also recommend off-station missions from time to time to find special technologies (or room/item types). This will help to stop the game becomming monotinous.
Good luck , I'll keep an eye on this blog and perhaps drop some more ideas in from time to time.
Hope this helps