They'll continue to make games for Nintendo as long as they live and work at Nintendo.

They are another Nintendo developer that needs to learn 3D (maybe they should recruit some programers from other companies?)..

titles like New Supers Mario Bros. Wii, Kirby's Epic Yarn and Donkey Kong Country Returns tell me 2D is JUST fine, also Paper Mario on the 3DS

I disagree just using the battles for example, all they would need to do is have your pokemon jump off the screen and push the opponents pokemon into the background. Then the various moves can have neat effects, like fire attacks could have sparks jumping off the screen. I think it would look great with 3D effects. 

and for side scrollers  as has been said just have the background actually appear in the background, and or add weather effects like snow flakes that dance off the screen.

I would be sad to not to see sprites any more I hope more games are made with sprites TBH whether it's great pixel art or gorgeous hand drawn sprites. 

Um, Virtual Boy games used sprites. Now remember it was the system tech that made the games unplayable, not the sprites. You still got 3D from them.

But sales already answers that 2D isn't going away just because of this.

Sprites or polygons, New Super Mario Bros 3DS could use the background as a whole new level with the 3DS.

1. The programmers and artists at these companies know how to do both 2d and 3d.

2. Games on the 3DS don't have to be in 3D.

3. Sprite based 2d games with a 3d effect is possible. For example, Nintendo is re-creating classic 2d games in 3d for download on the 3DS.

4. The Wii and DS has had ALOT of 2d games that have sold ALOT.