Massive fanboy, love all three games (insert standard ME3 ending caveat here) but when I think about it ME2 is probably the one I feel least strongly about. Some random thoughts:
- The thermal clips change was beyond idiotic in the context of the game universe. But I got over it after about five minutes because let's be honest, the unlimited ammo thing was completely broken in ME1. So I'm prepared to give the game a pass on that. And I think they got the ammo distribution about right too: yes your favourite gun would often run dry but that added a level of interest and challenge that I quite enjoyed, having to pick and choose when to use your secondary weapons or balance them more with powers etc.
- The combat mechanics were improved on ME1, but they're nowhere NEAR as good as ME3.
- I thought they went a bit too far with the streamlining of the RPG / character building elements, and again ME3 probably struck a better balance in that respect. But I did like how the classes all started to take on their own unique character and play styles. ME1 suffered a lot from that, where a few of them (Sentinel, Engineer) just weren't as good. ME2 made them ALL playable and awesome in their own right.
- I liked that there was a lot more variety in how the weapons worked too. In ME1 all weapons within a class were basically the same, it was just a question of how much damage they did and how fast they overheated. Your whole goal was just to get the Spectre-level weapons then game over.
- Harbinger and the Collectors were a pretty awesome big bad, I liked them a lot.
- Some of the new characters were awesome. Mordin in particular, obviously. Grunt too. And Jack. I don't even mind Miranda. Jacob didn't need to be there though.
Most of my problems with ME2 are story related I think. Killing Shepard off at the start of the game only to immediately resurrect him/her was pointless. I liked the destruction of the Normandy SR1 - that was cool, it showed the power of the Collectors, and it allowed a bigger and better Normandy to be built. But Shepard dying was silly.
The thing where everything relates back to the first game bugged me at the time, and still does. Like the asari on Illium who's upset with humans because her daughters were killed during Sovereign's attack on the Citadel, and it turns out one was the receptionist at the ambassador's office and the other was the greeter for the consort... it's funny when the occasional character comes up again, but I don't need to know what happened to literally every NPC that was in the first game. Bioware seemed to think we did though.
Most of all though I think it suffered from the inconsistency of having two main writers, neither of whom seemed to have a firm idea of the ending they were shooting towards. ME2 is FULL of narrative dead ends and contradictions, especially once you've played ME3. I mean ME3 makes the whole main plot of ME2 stupid - there was no longer any reason for the Reapers to have a special interest in humans, there was no reason for the Collectors to be specifically targeting humans, and the less said about the human reaper itself the better...