I would make six different versions of the movie, three with a male shepard, three with a female shepard, one each pure renegade, one each pure paragon, and one each be more than a little ambiguous...
Fascinating. So what you really want is some sort interactive medium where the viewer can choose their protagonist and guide their decisions?
It would be a science fiction movie that you could go to see six different times and have a slightly different experience every time. Much like players who go back for a second or third playthrough multiple times because they wonder "What would happen if I...?"
You can't have viewers controlling the decisions of characters in a movie, that just doesn't work. However, you CAN replicate the end result: that you can experience the events of Mass Effect a thousand different ways, that even if you've seen the movie before you can't be totally sure you know what's going to happen because you don't necessarily know which version you're seeing, or even if you do, the last time you went you saw the paragon version and you don't know what to expect from the renegade.
Like the game, the experience of the movie would be a film that you can't see just once. I might even be a real dick about it and fix it so that the DVD release only puts a single version on each disk so that you actually have to buy six different DVDs to get every single version.
FYI, filmmakers have been doing stuff like this -- albeit on a much smaller scale -- for years. For example "Clue" actually has three different endings that were totally randomized in the theatrical release, so even if you'd seen the movie already you could go to the theater a week later and be totally surprised who the killer actually was. I'm basically proposing the same thing, but doing it for the entire movie, not just the ending.