Metroid Prime is imo the best of the three, and still remains my favorite game ever made. While SM64 is heavily dated by its camera and OoT is held back by a rather barren overworld and questionable design choices that hamper replayability (Water Temple, Navi/Dialogue Speed in general, rather bland dungeon design), Prime played exceptionally well in 2002 and still plays exceptionally well today imo. The game still looks pretty good, the atmosphere, world building, and exploration are all still top notch, and the boss fights, while probably not the strength of the game, are still pretty fun and engaging with only a couple of sticking points. There's not a lot I'd change about Prime if given the choice, which says a lot for a game that's now 20 years old.
