Metroid: Other M or Federation Force, even though Hunters and the original Metroid II are worse imho.
Skyward Sword, even though it's one of the best and Spirit Tracks or Triforce Heroes are much worse.
Nuts & Bolts, even if it's a masterpiece (the worst Banjo is Grunty's Revenge even if it's still quite good).
Bioshock 2, even if Infinite is the worst of the bunch (still good!).
I guess Phantom Pain is now considered the worst of the main series, but Guns Of The Patriots is the stupidest boringfest in Metal Gear imho.
I have no idea why I read it wrong. I interpreted the topic as "titles which are considered the worst but actually aren't". So, well.