There's so many ways this could go wrong..
1. First-Contact War
I can see it working, but with the way human vs. alien conflicts tend to go (not just movies), the writers could just cram human emotion into every single place they can find.
2. "Badass" Ex-Marine
We all know this might happen. It's a non-canon story about an ex-marine who kills stuff, there's really no need to explain it. It wouldn't do any justice to the Mass Effect series or the Mass Effect universe.
3. Basing it on Shepard
Probably not going to happen, because the producers aren't idiots, and Bioware people are executive producers. But it still could.
4. NOT cutting characters (If based on Shepard or his crew)
It'd just be seen as a fan service. Fans of the series wouldn't enjoy it and newcomers to the series may be confused.
5. Taking itself too seriously
Not many ways to explain it, it's just taking itself way too seriously [no teasing or friendly joking (Garrus)]. The climax of the movie being plagued by lines such as "This is our time!"
OR the movie could be incredible just like Mass Effect and not leave plot holes or clash with canon. I'll try to stay optimistic