I'd have to go with ME2 for this one
It may hav been streamlined a bit too much, but I was happy not to have to put huge amounts of skill points into Electronics, First Aid and Deccryption (I'm a bit obbsessive when it comes to loot, and not being able to open containers displeases me). I also found that this made biotic classes much more fun. Maybe I was playing them completly wrong but in ME1 most of my abilities ended up being used as croud control while my squadmates had all the fun
I also enjoyed the way the Collectors were done. While in the first game, you fight the geth from the start and they never really pose much of a challenge. When you first fight the collectors, (especially the first time you encounter Harbinger) the way they force you to change from "Sit behind cover and shoot till nothing moves" to something a bit more mobile. The fact that you will almost certainly die on these sections on the harder difficulties makes claim of them being a threat to the galaxy viable.
I can understand why people think the main storyline needed more attention, but I think this is mostly due to Bioware not using their usual formula. (Opening location,Second location, a series of 4 locations to be completed in any order, event after 3 have been completed, penultimate location, final battle) I was actually pleasantly surprised to find a different setup for ME2. Plus, what the game lacks in the main plotline it makes up for it in the character missions.
The boss fights were also a big thing for me. The Geth Collosus and the Thresher Maw fights were much more epic than anything in ME1 (the final fight was kinda a letdown though, because A, It looked like a giant terminator and B, I had enough ammo upgrades to make the Cain viable)
That said, I found that Harbinger was a much less impressive big bad for this game. Saren was a well written bad guy, he actually had a believable motivation, and Soveriegn, who had about 1 section of dialoge in the entire game, managed to set himself up as awesome incarnate. Harbinger never really has a moment like this until the very end of the game, and by then you have been annoyed by him constantly spouting "ASSUMING CONTROL, THIS HURTS YOU" all game. And I cant forgive the removal of the Mako