BW and BW2 both made sense for the DS -BW were developed for years before release and were based on the DS, not the 3DS.
BW2 are a holdover - they're not going to spend extra time and money to make the first 3DS Pokemon games a simple third version.
BW2 even came out a few months ahead of when we'd normally expect to see the 3rd version (June as opposed to September in Japan last year). It seems they are the end of gen 5 with gen 6 likely to kick things off on the 3DS exclusively next year.
It wouldn't have been worth it to redo the graphics of BW from the ground up just for a third version on 3DS.
Now I do agree with you that they really didn't NEED to make AT for both systems. It's likely not meant to cater to those who don't have DS systems yet...they probably need the extra sales from the DS-only owners. They probably figure that many of the DS only owners are younger and likely watch Adventure Time on TV - also figure their parents know they watch the show and buy TV show based games. It's likely to get extra sales more than anything especially since this is a tv show game and thus not likely to sell as much as say New Super Mario Bros. 2. If there is a sequel though, I would expect it will be 3DS only.
I dont' think it needs to be on WiiU either - the 3DS is capable of A LOT. They could easily have a game much bigger than this on a 3DS cartridge. I'm not complaining about the game length or size, just saying they could easily fit a lot more while still keeping it on 3DS. Personally I prefer handheld games. I think a 2D on a handheld is more likely to sell than a 2D on WiiU. But I may be wrong on that last point.
I was actually suggesting that not for the technical supremacy, but so that the 3DS gets a boost in sales. The 3D would be an after thought. Unless I'm reading your post wrong, that IS catering to people who haven't bought a 3DS yet. Although it's not their fault, they were forced into the position... they are a 3rd party developer, it's not their job to sell 3DS's. Wasn't saying that it needed to be on Wii U, I was saying that if retro studios handled it that's where it would end up. Anyone who honestly thinks the 3DS can't handle it needs to play Kid Icarus Uprising. It's beautiful, it's fully voiced, it's pretty long.