Windwaker -> Twilight Princess (I hated the gimmicky wolf mode parts soo much that I couldn't even finish the game)
Halo 3 -> Halo: Reach (multiplayer wise)
Fable 2 -> Fable 3 (A lot of people hated Fable 2, but I loved it. Fable 3 though, I quit after less than an hour. Maybe I should give it another try)
BIoshock -> Bioshock 2
Pokemon Gold/Silver -> Pokemon Ruby/Saphire (Gold and Silver spanned two regions, so it was a huge dissappointment when that didn't carry over into the next mainline game.)