Not everyone intends to buy a Wii U, and the Nintendo 3DS is fully capable of supporting online multiplayer. Why gimp the version for the install base that's already been established?
Multiplayer is one of the key selling points of the Monster Hunter franchise. However, the series is somewhat obscure outside of Japan, meaning it's rather difficult for players in both the US, and EU to find someone to play with. With online multiplayer on the Nintendo 3DS, that issue would be rectified to an extent.