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Lamace said:
Prime 3 by an infinite amount. Prime 2 is easily the worst in the entire Metroid series (my unpopular opinion). Why? Well... (Inhales deeply):

It went overboard on the backtracking
Found myself going from one far end of one level to the far end of another, for a single item to make progress
Often cruel level design
Wonky morph ball controls
Platforming with wonky morph ball controls
The Spider Guardian (worst boss fight in video game history, nearly ruined the entire game for me)
Odd design choices (why does Samus do a back flip when hitting a wall while using the screw attack?)
Thought finding the keys in Prime 1 was bad? How about twice as many here, half of them being invisible?
Constantly wastes your time

God I hate Prime 2! Wish I didn't, but I do. No game has ever frustrated me more than Prime 2. Because it's such a good game, marred by poor design.

While these things didn't effect my enjoyment as much as it did yours, I do feel a lot of these things were major hinderances to the game.  I think the next big step in Metroid is something of a marriage between Prime 3 and Prime 1 where the action/story bits flow seemlessly into exploration sections as the story progresses, perhaps in a somewhat non-linear fashion as you prioritize where to explore first, preserving the best of both games.