Science-Fiction Games:
A bit of a nuisance to me is how often I see psionics. It seems like every other sci-fi-themed game has a psychic somewhere. Granted, when they're implemented well, they can be a good thing, but most of the time...it really just seems to me like an excuse to have magic in a game that would have otherwise had none or very little, which would have made it that much more believable.
Civilization (In General):
Combat is decided by an arbitrary "strength" system that can have results that make no sense whatsoever. For instance, I've seen a tank lose to 1800s-quality grenadiers (Both stat-wise and sanity-wise, it didn't make any sense either), a squad of paratroopers lose to conquistadors (Once more, no sense made in game terms, either), and numerous other stupid events. This could have easily been fixed for both balance and realism if units had armor types and had expenses tied to how advanced they were.
Also bad is that units don't mean anything when stacked. You can't have units fight together and units can't defend together. Considering how simple the game's combat is, I really doubt this would mean much in terms of system requirements unless you had eighteen million units going at it at once. And if this would be too conducive to stalemates, a simple limit to units in a particular tile could be added - honestly, that should have been there in the first place.
Dead Space:
Melee attacks were mostly useless. Granted, I know you shouldn't be able to just beat down anything in your path, but they not only didn't do much to begin with, they also put you in a more vulnerable position without sending your target back enough to keep it from coming right back to slash your intestines out. The stomp had some use in breaking crates or squishing the odd infant, but you still ended up taking more damage trying to step on a legless necromorph than you'd probably end up dishing out to it. Although, there is definitely a special kind of satisfaction to be had in killing a swarmer or divider part in mid-air with a melee attack.
The flamethrower was also significantly underpowered compared to the rest of the weapons. Regardless of how cool it looks fully-upgraded, the thing can put you in some serious trouble in tougher engagements.
This is mostly a nitpick, but a lot of the game's technology is effectively magic. But, again, this is just a nitpick, as they implemented it very well into the game's atmosphere and background feeling.
Portal:
The internet community ended up turning just about every phrase out of GlaDOS into a meme in some way. I've never seen one die faster than "the cake is a lie". Please, people, just cut it out. The funny factor died a long time ago.