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Vodacixi said:

I think Prime is better than Super. The only bad thing people keep bringing about Prime is the Chozo Artifacts quest... but to me it wasn't bad at all. By the point I defeated the Omega Pirate in my first playthrough I already had like 8 Artifacts. So the backtracking was minimal. Also, since they tell you where each artifact is, I never felt like it was something boring or tiresome...

I don't have any problem with Metroid Prime.  That fetch quest certainly is a bit of a slog, but it fits the epic moment you're building up to.  I still pick Super, though, for many reasons.  Mostly because it is a perfect execution of the original design began in Metroid.  It is a joy to traverse at all times, no point is too far out of reach to get there in moments (if you have the right ability or skill), and the game rewards you consistently for putting in the time.  I'm still enjoying in the last week honing a new speedrun path and trying to make sure how to fit in a 100% run around it.  

I will say this...if Nintendo would release that Prime trilogy and I would be playing it right now, I might be swayed toward the Prime camp.  But as it stands, my first love will always be Super and that's very difficult to override.