Landstalker did end up being significantly different and better than I thought going in. It has all the appearance of a Zelda clone. It ended up being far more a platformer from hell than a stabby adventure game, which I liked better except for those times the perspective or blind jumps made me want to kill something.
ToeJam & Earl: Panic on Funkatron is my pick. Raged against the format change just like everyone else, yet in the end, the game is better for it. The world is so much more vibrant, the characters better developed, and the dialogue and variety is wonderful. I believe all these elements could have existed just fine in the original format and have satisfied everyone, but as it stands, Panic on Funkatron is a great game which advances the series more than its familiar aping of the mascot platformer would initially indicate. I miss the Nethack inspired gameplay of the original, but Panic on Funkatron overall is a better game.