I seem to be in the distinct minority in that I would actually prefer a straight adaptation of the trilogy of games - it's a great story, and a new adaptation would give them the chance to put that f*cking ending right!
I'm pretty sure that they've already confirmed that the movie(s) will feature MaleShep. A shame, I prefer FemShep too.
Whilst they've only confirmed one movie, it's a no-brainer that they'll be hoping to tell the trilogy story over subsequent films too. If they do go down this route then the one thing I'm expecting is that they strip out a lot of ME2. It eliminates a number of superfluous characters and it removes a large chunk of what is essentially not that important plot. The only characters that are a real must from ME2 are Mordin, and possibly Legion. You could get away without including the rest.
It really wouldn't surprise me if they split the first, some elements of the second, and third games across a trilogy of movies. The problem with that model is where to finish the first movie. An obvious break would be to end the movie on Virmire. The question is whether or not they'd be bold enough to go with such a downbeat ending. Plus you're not solving the central problem posed in the story - stopping Saren.
Re the characters, I'd be disappointed if they morphed Kaidan/Ash into a single character, although it would get around the Virmire problem (people are going to moan whoever the movie kills off). TBF, I could see them doing that. Essentially after the Virmire decision those two characters are interchangeable anyway. Only question would be which one the movie went with - Kaidan to play up the 'buddy' role with Shep (although do they need that with Garrus onboard?), or Ash to play up the love triangle with Liara (although you could do that with Miranda if she turns up). Not sure. Given that one of the most important elements of the ME series for me has always been the characters, almost if not AS much as the trilogy's plot, then I'm reluctant to see them messing about too much with the characters.
I think at a bear minimum they'll have Liara (for LI purposes), Garrus and Wrex (for later Genophage purposes), Tali (for Rannoch purposes) and one of the Virmire two. Of the supporting characters, Anderson and Joker would be the big two that you'd have to have. The rest, Chakwas, Pressley, Adams etc, you could probably get away with almost cameos. Fans would pick up on the namechecks, whilst to casual viewers it would mean nothing but wouldn't take up much screentime.
I think whichever way they go they're going to have to just stick to the absolute core missions from the game. Even that will be too much, but there won't be any scope to really take much from the wider DLC. For the first movie, that won't be so much of a problem, but later on it's a shame that we'll likely not see anything from LoTSB. I guess they'll have to take a few things from the third game's DLC, particularly From Ashes and Leviathan though.
I'll be interested to see which way they go with a third movie if it's based on the final game. Particularly the ending. I'd bet my last $$$ on them going with high EMS destroy. Let's face it, after three movies there's no way they'll go with REFUSE. Likewise, I just don't see CONTROL being there either. Doesn't really seem epic enough as an ending. Sure, Shep dies, but that's it. There's no real downside beyond that. Destroy has the moral implications in that you're sacrificing EDI and the Geth. SYNTHESIS, while I abhore it, makes more sense than Control as the ending to a trilogy of movies. It's a fundamental shakeup of the workings of the entire galactic civilization, and the implications that that would bring. Also the moral dubiousness of actually making that choice on behalf of all other life in the galaxy. Given the general polarized reaction to DESTROY and SYNTHESIS, I'd be staggered if they went with SYNTHESIS. It would seem to have DESTROY written all over it.