I feel pretty confident that there will be a 2d Mario game both on 3DS and Wii U. Nintendo already showed that NSMB Mii demo for Wii U. Plus they seem to be big on 2D platformers right now, having releases DKCR last year and there will be 3 2D Kirby games releasing within a year of each other.
I think Nintendo had just planned on spacing out the sequels to the DS' big hits. This year we got Nintendogs + cats (which more should of been done with) and Mario Kart for the holiday. Next year we already know Animal Crossing is coming and then I expect at least one of Pokemon, Brain Age, or 2D Mario. With the other couple likely coming in 2013.
I just don't see any reason to think Nintendo is going back to ignoring 2D Mario again. If anything I think adding 2D elements to the 3D game shows that Nintendo knows the 2D games are more popular and are trying to increase sales of the 3D games.