MASS EFFECT
(1): The Multiplayer Unlock system. Random unlocks are always irritating as hell, and when you tend to want something, no matter what level of rarity it is, it always seems to take forever to unlock, at least in my case. The higher the rarity, the longer it takes. Seriously, Bioware, you can keep the random boxes, just give us the option to buy the weapons themselves on their own, if only for a higher cost!
(2): The fact that human romance scenes tend to be more drawn out and detailed than those with aliens. Ok, so they aren't human, big fucking deal. When all I get is a hand-hold from Tali, a headbump for Garrus, that's disappointing. At least Tali's romance was a little better in Mass Effect 2. Don't even get me started on 'Casual Garrus'. Wearing the turian equivalent of a smoking jacket and reading a book after, please.
(3): And lastly, the fact that the last missions on Earth didn't culminate into an extended Suicide Mission, only you got to coordinate your war assets for maximum effect. Now, the defense of the missile trucks wasn't too bad, it felt pretty intense at the end to me. But I'm sorry, the last mission's left a hell of a lot to be desired, regardless of the extremely lackluster ending. Damnit, Bioware, you forgot the saying, "Not with a whimper, but with a bang!"! I wanted Shepard to go out with a bang, if at all! But nope. Closest blaze-of-glory moment is given to Grunt, and although deserving, he still isn't Shepard.
HALO (mainly 4)
(1): This is actually for all but Halo 3, and Halo 4 is most definitely guilty of this, but 343? Make the Assault Rifle stand up against the other main rifles, like the Battle Rifle and DMR. In Halo 3, it was on par to the Battle Rifle, and in Reach, it was close to the DMR. But now, for Halo 4, I can rarely use it and get ahead. Everyone uses the Battle Rifle and DMR, and I'm getting kind of sick of the lack of variety. The Carbine doesn't stand much of a chance, the Light Rifle isn't much different, and apparently, automatics are shafted entirely unless its the SAW.
(2): The story of 4 is pretty good, I'll give it that, but it hinges a little too much on the extended universe. Now, I've read some of the earlier books. But some of the 'revelations' in Halo 4, such as humans having had a war with Forerunners before, and eventually becoming with the Prometheans, messed with my head a little since I didn't read the latest ones. "How did that happen? How long ago was this? If technologically advanced humans were around back then, why did we have to start all over again, and are where we are now with tech?". It was after watching the Terminal Videos in Waypoint (Yet another mistake, let them be watched in the game-proper, damnit!), that it made sense, and reconciled nicely.
Now, I'm all for incorporating the extended universe, so long as it's done well, and does not rely too much on the works outside of the games.
(3): LET ME PLAY AS A FUCKING ELITE. I don't care if you're supposed to play a Spartan, I don't care if they're the bad guys again in Halo 4, don't care. There are still some that are good, they are still aliens, and seriously, I was disappointed at the lack of Elite action for multiplayer.
Of course, I bring this up simply to pad out this particular list. Otherwise, I couldn't think of a third. What can I say, I love Halo.
Anyway, these are, mostly, minor gripes, since I love both series dearly.