Although I feel like things like this have more to do with noticing them the more you play them. Each time I've played through SotN, I notice a new flaw.
Shadow of the Colossus PS2 - frame drop issue
Katamary Damacy - should've offered a face button as alternate input for running
Super Mario Kart - needs more single player content
StarCraft - single player campaign might be a bit too hard for regular joe