Metroid Prime 2 or Metroid Prime 3

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If it was Prime 3 vs the Gamecube version of Prime 2, 3 would win automatically on account of its controls.

With the Trilogy version of Prime 2 it's closer, but Corruption still wins. While there's a lot of good things about Prime 2, there were also times when it stopped being enjoyable and became a chore. Prime 3, on the other hand, was entertaining from start to finish.