I haven't played Metroid Prime and got about 3/4 of the way through 2 before 3 was released. I had no problem at all. Actually it was easier to get into than 2, the story is well explained. I'm not a big fan of FPS, but the controls made the game for me, I'd play more FPS if they use a similar control scheme.
And yep you should buy 3 it's great.







