Like someone else said, you really can't go wrong with either.
I have played through both myself, and if I had to pick a favorite based on the single player experience, it would definitely be Metroid Prime. Halo is a fairly long game with great AI, but MP has sooooo much more going for it.
Here's how you decide, pick which experience you'd rather have:
- Halo: Pretty much non-stop shooting. Great AI playing with you and against you. Vehicles are part of the action, though not all the time. Fairly long game, a good 20+ hours.
- Metroid Prime: Is a first-person perspective, but mainly an adventure game. Of course, there's lots of shooting, but adventure is the main draw. One big 'semi' seamless world, lots of hidden goodies to upgrade your power. I beat this game with 100% right at about 15 hours I beleive.
Hope this helps.