Wow, I thought my thread was dead, haha now look at it.
The 3DS announcement does open some new doors of possibility, imo. And like ShadowSnake mentioned, while 2D Mario sells extremely well, the whole point of this new handheld is the 3D. That's the main thing, so I think a 3D Mario would be infinitely better suited to show off the system's strengths and novelty than a 2D Mario. A sidescrolling Mario on 3D screens would be pretty pointless, I'd say.
Just imagine the water splashing out of the screen whenever Mario jumps into a body of water, of the globs of goo and fire that enemies spit out, coming straight at your face. Those octopus-jetskiing parts... man, the rollercoaster-Mecha-Bowser-bossfight would be a sight to behold in 3D. So many awesome things that would be totally awesome!
Also, consider the rumours that 3DS will feature one or more analog sticks. 3D Mario is the reason Nintendo introduced their analog stick on the N64.
Seriously, imo a game like this would be a much better fit than a sidescrolling 2D Mario could ever dream to be. And besides, while it's true 2D Mario sells like crazy, 3D Mario games only seem to sell 'bad' when you compare them to their 2D counterparts. All 3D Mario games (including the 64DS one), have sold close to, or over 10 million. 10 Million! That's far more than 99% of every other IP out there could ever hope to sell.