When Capcom brings MH to the next generation of portables I think they should only make an exclusive series, or have 2 dramatically different series running (Monster Hunter Diary vs. Monster Hunter Portable instead of Monster Hunter vs. Monster Hunter Portable). Having multi-platform, or multiple similar series will create brand confusion, and most importantly, will hurt the franchise's largest selling point - local competitive play. By releasing mutliplatform or congruent series of a similar style, Capcom is opening up the flood gates to people buying the games on platforms their friends don't have, and finding out that they're not able to play with each other.
From a business perspective, I think it's smarter to bet on Vita, as you'll still have a secondary (first in release, but secondary in revenue) source of income via console releases (yes, I know they're not the big releases), since platforms similar in power to the 3DS will not exist for much longer. By going with Vita, you'd be having PS3/PC/360/Wii U console game opportunities. It would also allow more promotional mobile games, since Vita's technology will be assimilated into those (and other) devices within the near future.
Yes, I know Capcom's engine that works on 3DS, but I imagine it would be easier to bring them over to Vita than downscaling things to 3DS.