It would appear that developer Tom Happ is actively working towards that goal, as he has told Destructoid that the title might be heading to the Wii U next year - although the 3DS is much more of a "maybe" due to its unique hardware:
...can't commit to anything, but Axiom Verge will *probably* be available for Wii U in 2016. 3DS is quite a bit more difficult since the hardware is so completely different. Should Nintendo be reading this and decide to lend me a hand, that'd be VERY appreciated!!
Nintendo - give this man some help. We need Axiom Verge on our consoles!