It's actually a little sad that the deepest game you ever played has only been a shooter on game cube.

It is not a shooter. It is an adventure game. The mere fact that you say that tells me you have not played it. I've had better experiences, I just said it was the deepest game I've ever played. 

It's a first person shooter.

No, it's a first person adventure. 

Let's be honest, First Person Adventure was more of a buzz term than anything else. But it's definitely not a standard FPS.

Metroid Prime is still one of my favourite games of all time though, the way it told the story of the game universe through scanning was just genius. It left so much to the imagination whilst still giving lots of information about the world you were in... I just hope we see a new Retro Metroid on Wii U. The Pad could be a huge step forward on the scanning.

The difference is that the focus of FPS games is, well, Shooting. 

I'd say they are on par.

Counting Xenoblade, the Baten Kaitos series and other games they have done, Monolith Soft is a very good developer.

Retro has less games but counting their games which include two just short of classic revivals in Metriod Prime and Donkey Kong Country Returns which brought back two franchises that both hadn't had real love since the SNES it is hard not to say they have had the most quality.

But in general I'd say they are on par with each other right now and until I get to play Xenoblade Chronicles X and another brand new Retro game I can't say for certain which is better.

I take it you've never played the Metroid Prime (or Metroid series.) Metroid Prime is as much a first person shooter as Super Metroid is a 2-D Sidescrolling Shooter. Both games fit better in the Action-Adventure genre. 

I can't believe a game with hardly any  narrative plot/characters etc, can deliver such a stunningly engrossing world and story, purely from scanning the stuff you encounter. It's genius. I was completely absorbed.

No, Shadowgate is a first person adventure. Metroid Prime is clearly a first person shooter, its actual adventure elements are much weaker than most FPS titles today. Even Bioshock is far more passable as an adventure game than Metroid Prime.