The double genocide caught me by total surprise and it seemed rather weird that Lucas inexplicably went from being horrified at Sarah's bioweapon and wanting to develop a vaccine, to using the bioweapon to wipe out every human being on Mars aside from Helen, Tom & himself. It also seemed odd that Tanya talked Jason into releasing the bioweapon on Earth too despite the fact that I picked all the nice, humane decisions for her and Jason even accused her of being too nice just before their assault on Nanotech. I ended the game feeling rather disconnected from the ending since both Lucas and Tanya seemed very out of character when they each released the weapon.
A thing I plan to change is exactly this, let you choose what to do in the end rather than the game chooses for you. I started looking at the scenes and perhaps I could do it rather quickly without much rewriting. I wonder why I haven't thought about this sooner? 
1) This sounded very good to me.
2) I would have replied to this earlier but unfortunately you locked the old thread before I could.
3) Now that I've played through 0.9.3 I'm disappointed that you didn't address this issue as I continue to feel very disconnected from the endings of the game.
I think if you can choose what to do at the end, it should be in a certain way limited by what you did before, otherwise it could be unbelievable. For example, in Jade Empire, you could choose the whole time to be selfish or caring, but still at the end you could change it with one decision. That was quite disappointing for me, nice guy all the time and at the end bad boy.
I'm a firm believer in actions having consequences, but when the way you're limited due to previous decisions comes across as capricious, arbitrary or just plain out of character, it's even worse than when you're given a choice irrespective of your previous choices. At least you feel in control of your destiny in the latter case.
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For the record, I stuck to the same choices I made the last time around when I played version 0.8.3. Here are the results:
Version: 0.9.3
Scenes: 0, 2-12, 14-15, 17, 19-20, 22-24, 26-28, 30, 31, 34, 32, 37-39
Endings: Public Execution, Mystery Woman, Lost in Space
My game diverged when I hit scene 30 instead of skipping to scene 31 after scene 28 . Then instead of scene 35, I hit scenes 34 & 32, only to end with the same trio as before, 37-39. No Marsicide this time, instead there was a social fight that Tom won against Luke, causing Luke to kill himself. Gotta say, while the additional scenes gave me a better understanding of why Luke's feelings had changed, I still felt the transformation of the character I most closely identified with to be extreme, and I felt railroaded and dissatisfied by the ending.
I will play around a bit with the endings, but I felt like control of Luke was taken away from me to turn him into some sort of crazy monster, and that once again, as in the previous version, Tanya's genocidal behavior in the end didn't match how I had played her earlier.
and then the combined endings
