I think Prime 2 might be better. I just love how much better the boss battles were and the controls were.
Prime 2 is my favorite as well. Boss battles were as amazing a step they were abundant, the mood was decidedly more oppressive (fittingly so), and the abilities they included over Prime really made Samus feel like she recovered some of the versatility she lost in the transition to 3D. That said, I think all three are fantastic games. Still can't comprehend how some people think 3 is a disappointment.
For an on topic comment, I hate that this thread is hyping me for a new Metroid announcement at E3 when I've manage de to completely avoid such hype in the past. It just seemed that after all the (mostly undeserved) hate leveled at Other M, Metroid was destined for prolonged hibernation and, if anything, a 3DS release rather than a true home console iteration. Now, if Retro are working on a Metroid game it may be a 3DS game, but for all this time?
In any case if it's a new IP, I'm also all for it. What I really don't want is another 2.5D DKC game. Sorry at everyone who gets irritated by this, but excellent 2.5D platformers are far more plentiful than true 3D pathfinding games, so I'd much rather have the latter from such a talented studio.