I played the game through before many console FPSes and before getting used to the dual analog setup so at the time, I didn't find the controls that horrible after getting used to them... but nowadays, I think that control scheme would get awful. The actual gameplay wasn't terrible, I've certainly played worse, but the amount of backtracking needed was utterly ridiculous. The game seemed to be, "find this item, then find the next item on the complete opposite side of the map", in the 2D metroids from Super Metroid and beyond, there wasn't nearly this much backtracking, you were always discovering new areas, while right now the thing I most remember about Prime is running back and forth through that fire cavern trying to jump in first person. So yeah, while I was expecting the worst (turning one of my favorite 2D franchises into a FPS made by a rookie Western team) the game wasn't quite that bad, it was just dull.
I don't know how you can fault the graphics though, Prole, it definitely was one of the nicer looking and more atmospheric games upon its release. And the music was excellent.