I understand that the 3DS does have its limitations and with Xeno that some of those will be lifted but even if they are, Nintendo isn't one to change the formula if it isn't working out very well. Yeah, logically it sounds good design wise but financial wise is all that matters to Nintendo. I'm just devils advocate and Nintendo's spirit man because that's what they're thinking.

Again, you clearly don't know what you're talking about. Pokemon can not be accurately summarized like that, just like how you can't summarize every Metroid game as "You explore an unknown place, fight alien wild life, and recollect the same power ups Samus couldn't use at the beginning of the game for some stupid reason. Fight a couple bosses, something self destructs, the end." The games are supposed to be linear and you're not supposed to get lost. What are you even talking about? This isn't Zelda. Pokemon isn't an exploration game.

Legendaries aren't "shoe horned" into anything. They are integral to the ecosystem of the entire Pokemon universe. They are more than simple "super strong Pokemon" not. They have complex roles that intertwine deeply with the lore of each other and the entire Pokemon world. You're not supposed to "feel accomplished" catching and finding them. That stopped being a thing with "gotta catch em all."

You absolutely can not beat the entire game "with one pokémon and spamming the same attack over and over again," short of using easy mode Pokemon like a legendary or over leveling, which you can literally do in every single JRPG.

Every battle feels the same in Pokémon. And yes you can, I beat entire games with just Charizard. Instead of going straight to the second gym in gen 1 you go to Vermilion City on the ship to level your starter Pokémon some more. Then you go back and easily beat Misty with a fire type Pokémon. After that, any challenge is completely gone.

Every Metroid game is different.

In Prime 1 you were exploring an alien planet where the space pirates were your main enemy. In Prime 2 you're exploring a planet that is torn asunder by a multi-dimensional war between light and dark Aether. In Prime 3 you visit multiple planets and spacehips and work together with the federation. Super Metroid is a very non-linear game while Metroid Fusion is a linear story driven game. Metroid: Other M is a story driven third person beat them up with barely any puzzles or exploration. Every boss in a Metroid game feels different (ok, not every boss lol). In Pokémon there's no difference between "boss encounters" and normal trainers. They all go down as easily. Metroid games also have vastly different stories each time. Pokémon stories are all the same practically. With the exception of Black & White.

And Pokémon has deep lore? You're kidding right? There's barely any lore to be found in a Pokémon game.

It's because fans of Pokémon that keep buying the same rehashed titles over and over again that the Pokémon formula will not change for a long time.

Why, when they can already make the Pokemon game people want with the stregnth if the N3DS? 

They could do it with the strength of the original 3DS,  amazing thing were achived on the PS2 look at the Jrpgs it recieved like FFX/XII. The Original DS could handle much better 3D then what pokemon offered at the time and even during the 2D era's Nintendo acted like animated sprites weren't a thing. The point is they are always behind, not pushing the boundaries.  Just look at the complex animations and behaviours of creatures in MH4 made for the original 3DS, yet Nintendo can't manage fully rendered battle environments in X and Y? By now you should know that Nintendo aren't interesting in delivering a ground breaking pokemon experience.

They could do it with the strength of the original 3DS,  amazing thing were achived on the PS2 look at the Jrpgs it recieved like FFX/XII. The Original DS could handle much better 3D then what pokemon offered at the time and even during the 2D era's Nintendo acted like animated sprites weren't a thing. The point is they are always behind, not pushing the boundaries.  Just look at the complex animations and behaviours of creatures in MH4 made for the original 3DS, yet Nintendo can't manage fully rendered battle environments in X and Y? By now you should know that Nintendo aren't interesting in delivering a ground breaking pokemon experience.