I can't really say. Metroid, as a whole, is probably one of the most impressive series ever. In fact, it's one of the few series that hasn't been destroyed over time (like Sonic, Megaman, Tomb Raider, Resident Evil, etc.). It's revival and transition into 3D breathed new life into the series, and only strengthened my adoration for the games.
I do think the older games were much more difficult. I was playing the original last night, and I was screaming at the game. SO. FREAKIN. HARD! Oh, and Super Metroid is the best of the classics, IMO.
But then I love the Prime sub-series. I think the controls (especially the Wii controls) are fantastic, and I love the touches they add to the games, even the most minute ones. I remember when I first saw Samus' reflection in her visor and the drops of water running down the visor.... amazing. I love that they kept backtracking and puzzles. My only gripe is that the subseries isn't challenging enough when it comes to battles.
Really, I don't prefer one over the other; I love them all.
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