I thought that the scene had well and truly been set for ME3. The very sight of the Reaper fleet powering up and heading for The Milky Way was more than enough to make me emit a quiet, nervous fart.
That's all that needs to be said. The Reapers are now a bit pissed off and are now on their way with the intention of giving us an intergalactic arse-kicking. That said, nervous emissions of ass-gas aside, I would be standing on the top of the Citadel, assault rifle in hand and calling out to the Reapers: "Come and have a go if you think you're hard enough!"
I'm guessing it will be dealing with the aftermath of ME2 and what happens will depend on how you finished the game. It was made clear that Sheperd (if he/she survived) now has evidence of the Reapers (the datapad that Joker handed to him / her) or at the least, information that might help find a weak spot in their armour.
The Illusive man doesn't seem the sort to give up easily and I suspect he might want the Normandy back at least, which isn't entirely unfair considering it cost him a shitload of credits to build! I still want to know what the deal with his eyes is. My immediate thought is that he is a Reaper agent, like Saren only with slightly more discreet cybernetic implants. The only problem is that I can't explain why, if he was what I thought he was, why he would do the things he did.
Anyway, I will keep my ear to the ground and see what arises!
Wardy