Escort missions. They are a terribly idea. I hate them, always have hated them, and always will; I have never, ever, found a single escort mission I enjoyed. NPCs simply are not smart enough to be escorted safely. Best case scenario the AI is smart enough to go run behind me, sit behind a wall, and not move until the fighting is over.
Games with only one way to do things. This is why I'll play Deus Ex (the first one) until the end of time; I can do anything almost any way I can imagine, without one way being massively impractical or downright impossible. If I'm set up for it, I can run in and just shoot everybody, if not I can sneak around without firing a single shot, but neither way is absolutely "better."