My main complaints are thus:
1: The difficulty of getting a hold of a Collectors Edition that ISN'T already pre-ordered. DAMN THIS GAME FOR BEING SO POPULAR! Thankfully, I managed to last-minute pre-order one at Best Buy.
2: The fact that in multiplayer, getting a new character, a new gun, or an upgrade for a gun you already have is extremely hit-or-miss: You usually get either an upgrade for a class and race you already have, or one of the starting guns. But, I've heard that the retail version of multiplayer is going to have character and weapon packs, at least supposedly. If thats the case, awesome!
3: Not all classes in multiplayer were created equal. Yes, I know, some are very specialized, but some are clearly better than others. Not REALLY a bad thing, but for me, its just not fun playing as anything other than my Level 20 Quarian Engineer. Though, part of that is due to the fact that, well, shes a Quarian.
4: The changes of some weapons. Very minor complaint, don't get me wrong, but I remember the Mattock being more powerful, and a little more accurate. On the other hand, I also remember the Revenant being less accurate and more powerful. Still pretty damn fun to use one or the other though.
And lastly, 5: The fact that it hasn't come out yet. I seriously want to play this, and I want to play it NOW. March 6th can not come soon enough even if it was suddenly March 6th this very second, and I had the game in my hands at this very moment. Well, actually come to think of it, that might be soon enough, but you understand my anticipation and excitement regardless.