I love them both.
They are definately very different... Prime captures, very well, the essense of the great 2D Metroid games before it, with emphasis as much on exploration as on shooting. It was the best game I had played all that year (and I played pretty much all of the best one released for each system). The story is great and the action (once you get used to the controls) is second to none.
Halo (and moreso Halo 2) is much more a 'conventional' FPS but is better than most other console FPS's (and my PC ones) I've played on so many levels. Especially with halo 2, they strove to achieve this very cinematic feel, with some great semi-scripted moments, and a decent, interesting story. Also, the AI (both friend and foe) really lends a great sense of immersion since it can be VERY smart much of the time. On harder difficulty levels, it really forces you to think out every move you make (which most FPS don't do, IMO), and even the smallest firefight can turn into a 30 minute siege. Which is why I said SEMI scripted.... even the parts where you can tell they are scripted, because the AI is so smart and can and will react to every move you make, you can play thru the same section 10 times and it will feel like a different battle every time.
I love them both... well, all four of them actually (both sequels were fantastic as well), and can't imagine not having played all of them. I think most Halo people disliked Prime because of the lack of the typical FPS controls... and yeah I admit the lack of a free look did throw me off for a bit. Also, the first section of prime, aboard the ship, I found to be pretty boring... had I not payed $50 for the game, I'd probably have stopped playing by that point. But once you get down to the planet surface the game gets soooooo much better... but I think a lot of people just never gave it a chance past that first part. Their loss!