Portal: No Escape

This one will make the fanboys happy, but will leave most people cold. It makes the mistake of assuming you can cover for a lack of storytelling ability by having lots of Really Cool Effects, and referencing a popular game doesn't hurt.

It's not clear how our hero figures anything out. She just does.

It's not clear how any of this portal magic works. You're just supposed to know already, even though the character doesn't. Until she does.

It's not clear why the obvious weapon is never actually used as a weapon.

These are the kinds of things that aren't really useful as big revelations at the end, but need explanation as they happen.