I think the best thing about Metroid Prime was the atmosphere and how well they did the environment.
I think Retro was afraid to do a lot of branching/backtracking stuff like Super Metroid did because it was the first metroid done that way. MP3 does a lot more with using the space effectively to lead you around the way that the Super Metroid and after games do.
MP1 is still one of my favorite games ever. Can't wait to play it again in widescreen with the pointer.
Hey I finished batman, just gotta get all the riddler stuff now. The worst is finding those teeth! They're so small and easy to miss one or two. I think the biggest connection to Metroid is like I said, the sense of place and how the environment is used so well. Also putting little hidden shit everywhere you can't find unless you get this or that doodad. Also the detective "win visor" could be traced back to the X-Ray visor in Super Metroid, if you try hard enough. It's got a lot of other influences too, bioshock, splinter cell, assassin's creed, eternal darkness, ninja gaiden(in combat/counters, sorta) etc.