Headshots that don't instantly kill enemies.
Enemies that can take an entire clip of ammo to any part of their body for no reason. If there's a plot explanation (like with the Ganados) for it, fine, but usually it's done for its own sake.
Characters never eat, almost never sleep, and rarely drink liquids.
Hit points.
Any game that doesn't have region-specific damage.
Not being able to climb a chest-high wall, not being able to bust open a door (despite having all kinds of weapons at your disposal) and pretty much ANY game mechanic from Resident Evil (RE1, RE2 or RE0, specifically).