I downloaded this tonight, and I really enjoyed it. You've got a nice story going, and your level design is great. I love your use of cut scenes. I got up to the part where you rescue the fat guy, and then he gets shot, but I was killed by one of the dog aliens later in that level.
I've used Backbone a lot myself, and I understand the limitations of the program. It's a great program, if only it had all the bugs ironed out and actually finished.
I don't know if you still post here, but at least bumping this old thread (I only found it tonight during a "Backbone" search) might let a few more people see your game who might have missed it the first time.