*Minor ME1&2 spoilers*
I'm curious to see how previous choices effect the final game when we import our characters. For example, what if the humans are in charge of the council after the events in ME1, will this effect Earths fate, or if there's still a multi-race council will Earth be fucked due to the council's incompetence. I feel the Turians may be a valuable ally, and we may learn more of them. As a former enemy, having them as an immediate ally will be an interesting story element. Another interesting possibility is having the Rachni to call upon, if you made the good choice in ME1. Or furthermore, being able to end the genophage (sp?) of the Krogans to combat the Reapers, which would be an incredibly important choice to make, one that has great lore behind it. Or having the Geth on your side, or not, which could add religious elements to the story. One thing I'm most interested in is what of the ME2 companions. I don't think they'll be in the final game too much, what with them being able to all die and whatnot. But if anyone can incorporate them into the story, it's Bioware.
I think the possibilities for the finale of this epic RPG are boundless, and if Bioware get it right, they'll have created an incredibly deep and interactive story. There's an amazing amount of choices I can think of, and playing through all 3 games will be a real treat.