I guess it didn't really bother me. I hadn't really played too many FPS before that. I was bummed that they changed the space jump to double jump and got rid of the screw attack, for Prime at least. I'm not wild about the mechanics of the screw attack in Echoes. But I thought Prime captured the spirit of previous games. Plus the gameplay was really solid. Besides the cool storyline and bounty hunter chick, Super Metroid was what truly ensnared me about the series. The graphics were impressive for the time and the gameplay was unreal. The control scheme was just so perfect.
In the end, I am glad Metroid made the shift into the 3D realm. It is still more of an adventure game then a FPS, though it is literally an FPS because of the perspective. I think next it needs to incorporate some customization elements. I have some ideas, but I doubt Nintendo would listen.