Xenoblade's story alone makes it one of my favorite games of all time.

Truly one of the greats. I heard the Bioshock devs drew inspiration from it.

>but my point is true regardless of one's opinion on it

Not really. It's an opinion not a fact. 

Yeah, I definitely hope for Prime 4 , whoever is developing it makes a great story. I honestly wouldn't mind a more character driven Metroid Prime. One where a majority of the game is gameplay with lore snippets, but when a custcene DOES HAPPEN or when the story is represented it is on the same level as something like Uncharted. I don't think a lot of people can properly captivate the nuance between a mostly abstract and interpretive work, and one that's more story driven, so seeing a mix of that would be awesome. And of course the story should be interesting enough for the lore to have an impact on you deeply, other than just "oh ... this is kinda interesting"

I really enjoyed the EarthBound stories. But ill have to give it to the Metroid series especially Prime

Oh shittt. I forgot about this!!

If you have a brother, this game is going to be an emotional ride.

Ok. 

Fair enough, but I think retreading would be kind of lame. Doing characters right for the first time, while keeping what metroid was, would be cool af

Out of my limited repertoire with Nintendo, I am gonna go with the Metroid Prime series.

Agreed.

The core strength of the series is isolation and atmosphere, dialogue and traditional storytelling get in the way and break the mood.

Fire Emblem: Awakening (of those I played, of course).

Does Eternal Darkness count? Silicon Knights were a first party studio from 2000 - 2004, right? I dunno, but if it counts, I pick that one!

Otherwise it would be Majora's Mask.