Let's take my top 10:
Metroid Prime: The quest for the Gravity Suit. It felt very uneventful compared to any other part of the game, removed from the plot, from the Space Pirates or the Chozo ruins, trekking through the wastes of Phendrana. You also had to deal with pre-gravity suit water physics heavily, which was just an irritant.
Sonic Adventure 2: Route 280 and Route 101, the driving levels. Just plain dull.
Super Mario 64: Dire Dire Docks was a pretty bad level, too much drowning risk and not much to do compared to other areas.
Super Smash Bros Melee: Race to the Finish felt pointless compared to 64's. "Snag the Trophies" too was not really needed at all.
Pokemon Gold and Silver: Pryce and his gym.
Mario Tennis: the volley challenges against the Pirhana Plants
Fire Emblem: Radiant Dawn: the Grann Desert level with Micaiah's Army (Chapter 4-3)
PSO Episode I and II: The first two areas of Episode II, just "training simulations" the lot of them. It felt like a really cheap way to pad content on, especially when they just as easily could have made them part of the planet's surface and better-integrated them into the plot. Olga Flow was an interesting concept, but half of Episode II was "training mode"
Super Mario Galaxy: Manta Ray Racing, full stop.
Super Smash Bros Brawl: Any "original" boss in SSE. Those robot-y guys and Tabuu were just infuriating at times.
Monster Hunter: pissing me off since 2010.
