Overly Simplistic Bosses
Now, this is, to some degree, the opposite of the previous pet peeve stated in that this is where bosses don't really feel like bosses.
In Saint's Row 2, the boss fights against the two Ronin involve the player being forced to use the katana. The player cannot swing wildly like it's fight club, however, because the bosses are good enough to counterattack.
You also defeat the bosses by counterattacking them (this is, in fact, the only way you can beat them). This means you have to simply time your attack properly a few times and the boss will fall over stone dead (after the proper "killing blow" animation, of course).
The boss fight you encounter in the fourth Samedi mission is similarly simplistic and repetitive - flash and smash, then rinse and repeat until a certain triple-platinum has become triple-lead (and triple-dead).
The fact that two of these three boss fights aren't really mentioned after the fact means that they, for me, felt a little... underwhelming. It's like the inevitable fight with your own dad in AC3, where a number of players actually wound up committing patricide before the victim could finish his little speech. It's like the inevitable killing of the man arguably responsible for Connor's murder spree - it doesn't feel all that great. I'm left feeling like JC Denton sounds after one of the Rentons is killed: A bit sad but relatively emotionless.
Inaccurate Cutscenes:
This is more of a pet peeve than an actual flaw that I'd deduct major points from a game review for, but inconsistent cutscenes always bug me. For instance, in SR2 (I've been playing that frequently as of late), there are two missions where your HQ is attacked. One takes place mostly outdoors, yet the post-mission cutscene shows all the relevant characters indoors. The other takes place without any colleagues aside from recruited homies, but the post-mission cutscene shows that Johnny Gat was fighting at your side the entire time.
Also, in MGSV: The Phantom Pain, it's possible to take Diamond Dog combat personnel into story missions, but they always (somehow) turn into Punished "Venom" Snake during cutscenes. Again, small but annoying.
Also, everyone continues to refer to you as "Boss" even though "Boss" is obviously referring to Venom Snake.