Does it count if it's the second entry in a series, with a return to the original's set up in the third entry? That could disqualify Zelda 2, US Super Mario 2 and Castlevania 2. They were different, but there wasn't a lot of history to deviate from at the time.
Castlevania 2 did introduce some elements of the Metroid style that lead to Symphony of the Night, which would also fit and essentially established a new standard for the series.
Is Metroid Prime's transition to 3D enough of a difference, or was it still enough of the standard Metroid gameplay?
A lot of gameplay mechanic changes in Gears of War: Judgment that were not welcomed by the community.