Mass Effect 2 is a brilliant game. No, scratch that, an incredible game. But it has it's warts.
[b/]Planet Scanning[/b]- I really don't understand why this feature exists. It's just a massive pain in the arse. It's too slow, involves no skill what so ever and it's just boring as hell. Why not just have more minerals rewards in the side missions?
[b/]Loading Aboard the Normandy[/b]- I have no idea why the loading screens aboard the Normandy exist. They are rediculous and really, really odd. It takes maybe 20-30 seconds to load the citys and most main missions. It takes the same amount of time every time you use the lift to go to a different level on the Normandy. What. The. Fuck. The Normandy should be one instance, load it all once you come aboard, end of.
The loading in general is epically long, I'd rather there where 3 or 4 disks for Mass Effect 3 if it meant shorter loading screens because those things are incredible.
[b/]Male Shepherd[/b]- How can you have a game full of so many voice actors, nearly all of which are better than half the games out their and have arguably the most important character voiced by a plank of wood. I get some people might be pissed but just change him for the final game. He's awful. Have Nathan Drake or someone to do it, god knows he's proved his worth in this type of role. Without some juicy lesbian goodness in Mass Effect 2 this is especially irritating.
[b/]Too few Weapons and Armor[/b]- I very much prefer the inventory system in Mass Effect 2. No more fidderling around with 200 different armor types and upgrades, thats great. The research system is a brilliant way to cut down on this. But they cut down WAY too far. I've completed the game twice, now on my third and I have 6 heavy weapons and 2 of every other weapon. Even one more of each weapon type would have been enough.
[b/]Side Missions[/b]- I like the side missions. They're no Fallout 3 but they're decent enough. The problem is this; if you play any of them before the suicide mission your unwittedly punished.
Let me explain. Though out the game there are several unavoidable main story events. These events are triggered after a certain number of do-at-your-leisure missions. This is a fair way to plan out the game; it makes the story more urgent and adds a certain extra layer of challenge. The problem is that the side missions, that have very few benefits, also affect this timer. This isn't such a problem for most of the game, but if you don't have all those characters and loyalty missions down when the last of these events hits you know it's a problem.
A little thing to fix for the final in the trilogy.
[b/] Subject Zero was Disappointing[/b]-...Look, ok, this is a little petty but I was kind of annoyed by this. Not so much annoyed just kind of..."Ahhh. She's crap". When you first rescue subject zero you see her destroy 4 giant mechs BY HER SELF! Brilliant! She had to be sealed in the status in a high security prison IN SPACE! Awesome! She's possibly the most powerful human biotic alive!
...So why do her powers consist of shock wave and lift? Why is her special power Biotic bullets? Why is she piss weak?
Ok, it get that she couldn't be nearly that powerful or the game would be come too easy with her around but still...At least give her something cool, like a power that maybe rips people appart or something...
Actually this could go towards all characters. More unique skills and powers for each, it's an improvement on the original but hey...I'm never satisfied.
Most of these problems are tinny little specks of grim on an absolutely wonderful game. Sort them out and Mass Effect 3 will be incredible beyond words.
EDIT:
[b/]Scrape the Paragon/Renegade System[/b]- I'm not meaning the whole idea. I like the way Mass Effect 2 handles alignment with the whole good cop/bad cop idea, and the way it's handled with the speech wheel is very clever and organic. But there are some serious problems.
First of all, the more Paragon and Renegade you are, the more speech options it unlocks, some of which are vital to get the best result out of your game. That right there destroys the whole concept of the decision making. If I see an option I should be able to choose which one feels right to me. Instead I find myself sticking with one option though out the game rather than making decisions so I can get the benefits later on. Key dialog moments should not be decided though how often you picked the high or low option in conversations. You should have too look at the situation, the characters and the options and pick one that seems right to you.
Also the Scaring system in this game was just tacked on. It makes very little sense in a game like Fable, even less in more believable world like Mass Effects. No tacked on explanation that makes no god damn sense is going to change that. It's also another factor that effects decisions you should be making on your own terms.