Well, it's a far more competent effort than Dragon Age II by far.
Really I have only three complaints the first is:
Interviews said that multiplayer wasn't going to be mandatory for getting the best endings in singleplayer. However, the only way to increase galactic readiness is to play multi otherwise war assets are at half strength. The best endings require a war asset rating around 5,000 or so and the cap seems to be around 6,000 so... you can do the math.
The other two issues are SPOILERIFIC:
Kai Leng. I'm probably a bit poisoned to the character because of hearing how bad the novels with him in it are. But it seems like a case where the writers and artists are trying too hard to make him some sort of badass. He would have been better if introduced in ME2 as someone shadowing you for the Illusive Man.
My main issue with him is on Thessia where it's supposed to be this massive defeat but it's really just him and a gunship and other than act of plot I would have had him. If say he planted explosives throughout the whole building and it came down on you during the fight while the gunship was doing a strike it would have seemed like less of a chump thing. They needed to establish better that yes, he had total control of the situation and you were completely screwed.
The second major issue with the plot:
The damn kid! I was fine with the cheap shot emotional death. But the dream sequences just took you out of the game. Shepard turning in bed hearing their voices would have done the same thing without trying to seem "artsy" and cheap at the same time.
But the nail in the coffin was having the Catalyst look like the damn kid. I'd have been happier if, in fact, it was a conversation with Harbinger affected by the Crucible. It'd also have been nice to see them using it as a relay from darkspace, summoning the rest of the Reapers to Earth and hammering home that this really was the last chance to stop them. Having a Reaper controller AI on the citadel just seems like it introduces too many questions that they don't answer unlike vigil. It still could have been handled fine, but just about any representation other than the kid as "your collected guilt" would have been better.
This seems like Square-Enix crap.
Okay I lied, one other big issue bugging me:
The Normandy crash landing thing also made no sense. Unless the Crucible is damaged and going to blow Earth up why the hell would Joker FTL? If Shepard got a comm through to him that firing it might hurt EDI I could see Joker going rogue, taking the ship out of the battle and trying to run away irrationally. A line or two of dialog after Shep's decision could have covered this. As it is, it felt like the ending of Knights of the Old Republic II.
It feels like the Normandy re-seeding humanity was supposed to be for the worst possible ending, and proper "Shepard's burial on Earth" and "Shepard's funeral on Earth and oh wait here s/he comes!" endings were supposed to be made but left out.
Honestly my main plot complaints are the Square-Enix crap
Kai Leng trying to be badass
and
the kid as the personification of Shepard's guilt
. Overall though it wasn't as intrusive as the nonsensical fights in Deus Ex: Human Revolution or its nonsensical end fight.
I do have a few intellectual issues with some directions the new writers took though:
Basically individualistic AIs being viewed as inherently superior with the Geth being re-written to be like EDI. The most interesting thing about the Geth was how they were totally different cognitively but could still be reasoned with. The way the writers treated AI left a bad taste in my mouth, especially as a Shepard hell-bent on preserving *ALL* sapience. There should have been more of a moral dilemma around letting Legion re-write the Geth to his template based on "doesn't this go against your own ability to determine your path as an overall species that you originally planned?" Which is also why the 'renegade' ending seemed like the only proper moral option.
So, one bad design decision. One WTF? thing, but overall my complaints are more issues of some of the directions they went with some things which are utterly balanced out by:
Tuchanka and Rannoch pure awesomeness
.