Black & White series, the sequel introduced new features that made things interesting but fell short of the original due to lack of features that made it so unique, and also lack of multiplayer/skirmish.
Crysis series. Crysis 2 had completely different aliens and a completely different nanosuit, despite it being a nanosuit that was featured in the first game (Prophet's nanosuit), and also made the suit some really dumb bioweapon because apparently it's easier to generate genetic codes in a nanosuit instead of a laboratory.