It's a FPA.
The most important device in the game is the scan, not the guns.

It's an FPS, since most of it's gameplay elements are centered in Shooting.

In comparison, a true First-person Adventure is more like Portal or Penumbra

It's an FPS/Action-Adventure hybrid. I don't see why we have to classify it as either an FPS or an FPA. It has elements of both game types.

The beams and missles are used more as tools than they are as weapons. Like the portal gun in Portal.

Does it really matter? A game's a game, whats the classification have to do with anything? What type of game is Spore? Will its genre name affect sales at all?

Well, if you really want to debate it though...

- Your have a first person view
- The majority of the game, essentially every single room, has you shooting

Pretty simple. FPS.

Adventure, even though you are constantly shooting, that is not the main focus of the game.

Your first point bears no relevance since FPA is, well, first person. Your second point is up to debate, but many would argue that the main point of the game is to unlock various puzzles and proceed. Heck, you have to do all those stuffs in boss fights and not just shoot to win.

As far as I'm concern, whether Metroid Prime is a FPS or FPA does matter. I mean, why classify games into different genres? Personally, I consider Metroid Prime a FPA game, and not something a FPS fan who does not like puzzles or adventure games would enjoy. Now, let's imagine a scenario such person comes out and asks whether Metroid Prime would suit him/her or not...

Shooting isn't where the game stands out anyway. If it truly is a FPS, it certainly wouldn't be so critically-acclaimed.

I agree with LNRT. The rest of you guys don't know what the hell you're talking about.

*buys LNRT a beer*

It's a first person shooter, but it's not a First Person Shooter.

I think it's a game that's in the first person. It has character development and you can shoot things. Games don't fit into perfect labels, just like people don't. Metroid Prime is a great series, and that's all that matters.