My title of choice would probably be Daggerfall because it’s just so ambitious and truly offers an experience none of the other elder scrolls games offer. That being said it is kinda an example of a sequel eclipsing it’s predecessors as well given it is more or less a straight improvement over Arena in every way.
Probably Commander Keen: Invasion of the Vorticons. I loved that game but the next title was Keen Dreams which didn’t feel like Commander Keen to me. The third game Goodbye, Galaxy did turn it around though and was probably my favorite in the series.