Chiming in a little late. Hopefully you haven't done anything drastic, but here is, I believe, your solution:
On the WiiU, make a seperate account. Each account has seperate saves for all the games being played. When you want to play your version of MH3U, switch to that account, and play.
On the 3DS, download the transfer tool, and transfer your file to the WiiU under the new account. The 3DS will be empty of a save file, so when you are ready to play on the 3DS again, just open the transfer tool on the 3DS again, and transfer your file over.
When you want to play with your friend(s), just have the WiiU player make the multi user room, and you and your friends join in.
Anytime down the line that you want to play on the WiiU, just switch to your account and transfer the file to the WiiU and so on.
Good Hunting to you.