I do at times have to struggle to play ME2 particularly when I know I have to run a mission of which I'm not particularly fond. I also think that the main story in ME2 was much weaker and diluted by all the character sketches with which we interact. I think BioWare could have solved some of this by changing the game's progression. How about playing it this way: ME2 -> ME1 -> ME3?
You're an N7 assigned to investigate the mysterious disappearances of human colonies that the overall galactic power structure doesn't seem to care about. Instead of Garrus, you get Nihlus, a SPECTRE quietly investigating the colony disappearances and increasingly evaluating you for SPECTRE potential. You find out early on that the colonies are being abducted by a mysterious race called "Collectors" who some believe come out of the Omega 4 relay from which no ship has ever returned. From then on, you spend your time assembling a team of specialists to help you survive going through the relay and investigating/stopping the abductors.
At this point because we're all new to the game and the franchise, we can be squarely focused on the Collectors as the root of all evil because we legitimately don't know any better. We can spend much of the game investigating/assembling the team and earning their trust because we have a whole universe to explore and discover. It is all new and exciting. Meanwhile, people come to the forums and post endless threads about who the mysterious Harbinger is and what it all means.
Then, you go into ME2 where you discover that the systems Alliance has decided to recommend you for SPECTRE assessment, and that Nihlus just spent an entire game assessing you. It was one of those "operations together." Then, during Eden Prime, Nihlus is murdered by Saren. Now, you've spent an entire game developing a relationship with Nihlus. How much more do you suddenly hate Saren? And then, you report to the Council where Saren treats you like crap. It feels that much better to prove that Saren's dirty because it's had direct impact on you, and then you wrangle out SPECTRE status and the game proceeds.
Finally, at the end of it all, you discover that the real menace was never the collectors, but instead it was the Reapers, and one single Reaper manages to nearly destroy the fleets of four species before it goes down. Now, you know there are hundreds, if not thousands, more Reapers out there heading to the galaxy. How hopeless do you feel? You won a single Pyrrhic victory in the face of overwhelming odds. Maybe, you've put off doomsday for a few years ... maybe.
Then, you have ME3 ...
Now, obviously characters and plot elements would have to be juggled and re-written to make this fit, but the more I spend time thinking about it, the more satisfying it feels in terms of a story and a trilogy.