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 original Deus Ex is still amazing and has definitely held up better than the immediate sequel, Invisible War. The Eidos Montreal sequels have their charms and are definitely more accessible to modern gamers, but lacks the flexibility for emergent solutions that you could come up with in the original game.