Firstly, Mass Effect would do far better as a TV series than a movie. The story is already neatly formatted into episodes, and that's true of all three games. A TV series would allow the inclusion of all the characters, and would provide ample time to establish the backstory of the universe. Sadly, they seem determined to make a movie instead, so I'm working off that assumption.
Firstly, I agree with most of what Reverend
said, even the part about leaving out main characters. As a huge Garrus fan, it pains me to admit that he's not a necessary character and could easily be written out of the whole trilogy, but a small role for him and Tali would be best for ME1.
I don't think there should be a prologue, the brief text-based infodump from the game is enough, and somewhat reminiscent of Star Wars. Explaining the history and depth of the Mass Effect universe can be left to the games where it can be explored fully at the player's leisure.
I like the idea of including Cerberus into the Peak 15 section of the story, but I don't see the point of including the Thorian at the expense of the Rachni. The conclusion of the Rachni arc in ME3 was certainly underwhelming, but they still mean more to the Mass Effect universe than the Thorian ever did.
I think that Eden Prime, the Citadel, Noveria, Virmire, and Ilos may be too many locations to include in a 2-hour action-flick, so merging the important sections of the Virmire mission into Noveria may be necessary. I also think returning to the Citadel before heading to Ilos would interrupt the flow of the story, going there directly from Virmire/Noveria would be best. You can still include Shepard defying his orders, just do it over the comm instead. We'd miss Anderson punching Udina in the face, but that's small potatoes compared to losing the awesomeness that is Garrus.
Finally, I like the idea of a post-credit sequence, but I think the reveal should be the Illusive Man. Take that scene between him and Miranda from the start of ME2 and attach it on to the end of the first movie instead.
In the end, what we are left with is a butchered carcass of a story that's missing some of its best characters, best scenes, and interesting backstory.