[quote name='AdamInPlaidum']I voted for Metroid Prime myself, but if anything, this poll has reminded just how good the Metroid series is. Not one weak link in the series.[/QUOTE]
IMO, Metroid Fusion comes pretty close.
Nothing like having a linear Metroid, where the computer had to give you hints and details about where to go. Metroids for me are about exploring every nook and cranny figuring out what to do next... getting told exactly where to go and what to do ruined it for me a bit. I enjoyed it, but it wasn't nearly as good as any other Metroid.
At least in Prime 1 and 2, the help system could be turned off, which was pretty awesome, made it feel more like a real Metroid, with the whole exploring aspect.