Not really the 3DS is getting to Monster Hunters despite poor sales. Wii got Monster Hunter solely for cheaper development costs not because of sales. I'm pretty sure it will, Monster Hunter's on PS2, PSP, Wii, 3DS, PS3 and even the Xbox 360 so I think are chances are pretty good. Heck Capcom said they were going to put it on the Nintendo DS but it wasn't powerful enough so they went for PSP.
The 3DS sales haven't been poor. Currently the handheld looks to out pace the first year sales of DS. The thing is regularly the top selling hardware in Japan since the price drop. Nintendo simply didn't push hard enough with the 3DS to maintain momentum at its previous price, but the DS suffered similar handling. Monster Hunter is a Japanese focused franchise. This is why I stated that the only way Wii U would get a Monster Hunter release is if the Wii U sells well in Japan. So much of the Japanese market is handhelds thus why this franchise with most of its focus in Japan has for the most part stuck with handhelds this gen. Monster Hunter for the 3DS is a natural fit for the Japanese Market. Monster Hunter for Wii U not so much. We'll have to see if the new controller helps the console create a market significant enough to warrant Capcom making a Monster Hunter game for the console.
Monster Hunter originally went to the Wii because of the franchise's Japanese market focus. There simply wasn't enough of an audience for the franchise to warrant HD developing costs because primarily the Japanese console market is too small to warrant that sort of investment. Wii U is going to have to over come that issue if Monster Hunter is ever going to grace its library. The touchscreen controller may very well help the console in that regard.