I've also thought of one more example.
Megaman.
Megaman 2 is considered by most the best Megaman game.
There is however a group of people who disagree... this group is largely populated by people who started with MM2.
After playing MM3 and MM4 first it's harder to appreciate MM2 because of the lack of slide and charge buster... even though MM2 is considered superior in pretty much all other aspects.