um... how could you possibly say Super Mario Sunshinre or Shenmue?
Super Mario Sunshine had a bunch of levels that required some stupid trick that you hadn't been taught to get anywhere, or it was terribly straight forward, yet obnoxious to get where you needed to be. The last few levels were an utter pain to get around, even knowing what you were doing, not that the other 4-5 were terribly exciting or challenging.
And Shenmue? What??? Wherever you needed to be in the game, you were always an obnoxious run away from it. There weren't really any shortcuts worth using, it was a bunch of walking through similar looking city streets. Shenmue 2 was even worse. A bunch of long runs through similar looking city streets. Even the cities you spent 15 minutes in had terrible layouts in terms of game design.
PoP:SoT and Psychonauts had excellent level design. Outside of a few hiccups (the area where you had to push boxes and jump around on rafters in PoP... that was just bad. There was no way to do it quickly, and the mailman & actress stages in Psychonauts, same thing, there wasn't really a way to do them quickly, it was a bunch of wasted time running from area to area. Haters of the last level be damned, I like my platformers to have challenging final stages).
Castlevania: Minuet of Dawn or whatever the US name was had good stage design, also. Not too much wasted time, once you were stronger than enemies, you could just run past them. Or fly past them, depending on how far you were.