It IS still in the minority though. the majority of the Metroid fanbase in fact, are now bitching about Other M, and how Prime was "sooo much better." 
I think the original Prime was really something truly unique. It brought Metroid to 3D perfectly- as well as it's atmosphere. loneliness.
2 messed that up with the annoying dual world gameplay, and 3.. while fun to play,rather killed the atmosphere that made 1 and 2 so unique.
My sentiments exactly. The first MP was absolutely phenomenal. I loved how every room was different, loved how each room had it's own things going on.  It was a great game for just sitting back and exploring, admiring the overwhelming amount of detail. Boss battles were done really well too. The final Prime battle really felt like an old school 2D battle brought into the third dimension. And the Chozo statues were pretty much how I'd imagined them as a kid.
Then Prime 2 came along. While I enjoyed the scanning in the first game, Prime 2 kicked it up a few notches. I felt that at times I couldn't walk 5 feet w/o having to scan something. I too disliked the light/dark worlds. If they wanted to do something wherein some of the boss battles took place in a dark dimension, fine. Making it half the game, bad idea. But what I hated most about MP2, what 
really got my goat (and choked it), can be summed up in one word.
Ammo.
Yes, missiles (and super-bombs) use ammo, but that's it. Using cool different beams at will (once acquired), is one of the hallmarks of the series. W/o it, I ended up using the boring old blaster for the majority of the game. Got REALLY boring.  About half way through the game it started to really piss me off. Prime 1 had weapon usage and acquisition down pat. Prime 2 pooped in our pastries in this department. Some of the weapons were cool, but the very limited ammo for them until almost the end of the game pretty much blew the neighbors dog. 
Loved the Light Suit design though, and some of the bosses were great. Enemies were interesting too, and the screw attack looked great. Would have liked to be able to use it al will though.
Still haven't played Prime 3. One of these days perhaps, when I' finally get a Wii.