I was playing old games (90s and early 2000s) in rencent few years till now. So I can understand how you feel and here's the reason: you are looking backward with a NEW or PRESENT method, or viewpoint.
When palying old games, I keep telling myself: you should consider the circumstance the game was created at before you judge it. If you take the present point to old things, most of them are outdated.
I'vs played 10 main titles of metroid, except MPH on DS and FF on 3DS. So I think I have some sort of right to discuss this one of my favorite series.
Prime 1 was definitely a great game at 2002. Before this, I doubt you could ever play a 3D game which has FPS, puzzles and exploration these elements FUSED together and still be with such a high completion. This game is definitely pioneering at 2002.
You mentioned controls are broken. Maybe you just COMPARED Prime with Halo, or some present FPS game (with modern FPS control). With nowaday opinion, left stick TURNS character left or right rather than MOVES left or right and right stick does not control cursor seems a little dumb. Yes I agree with this. But with existence of LOCK ON, I feel this dumb control acceptable.
If you are really feeling this control so bad, you can try Prime trilogy on wii, that's way more comfortable.