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.
The megami tensei series has some interesting moments like this: to start with, the fact that one of the spinoff series, Persona, is arguably much more successful than the mainline games. I think which of the series is better is up to any given individual’s tastes, but I’ve spoken with many persona fans that have never touched a mainline entry.
Following up on that, I believe that P4 Golden is better than P5/P5 Royal. Don’t get me wrong- P5 has a better soundtrack and is visually striking, but I think P4G gives the player more freedom and has a more cohesive story. Additionally, I think P4G nails the Jungian themes better than P5/P5R. I believe both of these entries are top-tier games, I just also feel that P4G is overlooked in favor of P5R when P4G does nearly everything as well as or better than P5R outside of presentation.