When i first played metroid prime, i was enamored. However, after playing it a couple of times, i was less excited. In hindsight, I think the purposefully crippled control scheme was a bad choice. But hey, MP3 will be free aim! yeah!
halo on the other hand i never really understood. I think there are a lot better multiplayer shooters on PC. Plus, halo is butt-ugly, and the level design on the single-player is atrocious.
so, i'd have to go with Ninja Gaiden Black for Xbox. But if I only had these games to choose from, I'd go with Metroid Prime. The sequel, while tougher, was more confusing, and the poorly-implmented story only served to slow the game play down.