Spoiler (highlight to read):
You know the more I think about it the more disappointed I am with the story on the whole, simply because there wasnt one.
The story from beginning to end: You recruit a bunch of team mates then attack a collector base.
I mean sure while I was playing I didn't notice, because the game itself was full to the brim of stories for each character, which was great and extremely well done. But the story on the whole, the continuation of the 'Reapers coming to attack earth' thing was really lacking. It's not a big Sci-Fi epic, it's a collection of short stories.
To put what I mean in perspective:
In the first game you discover the prothean beacon, you learn of a threat, you travel to various planets and slowly discover that it's not just the Geth that are at work, but an ancient race of killer machines who want to stop life from becoming too complex (or just destroy them all, I dunno, you never learn their true motives), you then discover that the citadel and all the mass relays were also built by the Reapers as bait for intelligent life and that the Geth and a reaper are about to attack. You then fight off the reapers as they attack the Citadel and buy humanity some time for the inevitable invasion. Awesome stuff and while I hate the way the word has been overused lately, it was rather epic in scope.
But Mass Effect 2 was just:
You recruit some squad members and attack a collector base.
Again, dont get me wrong, I loved it and played for 10+ hours each day since I bought it until I finished it. But the story just wasnt there. At all.