Metroid Fusion is my pick. The way the areas eventually open and get connected at the end is fantastic. The game builds a set of rules and you get used to them. So you navigate from a sector to another, eventually come back to a previous sector. But everything happens through the main hall with the elevators.
Then a some point, the story takes a turn and you end up going from one sector to another directly, seamlessly, and you are not expecting it. And at this very moment, the game breaks the rules it had set for you, and honestly, I found this to be excellent. You eventually realize that absolutely everything is connected, and several passageways are totally optional.
Legendary game. When you are used to such standards, shit like Dread is unacceptable.