I don't really understand the "segregation of the userbase" explanation, even for a local multiplayer game. It's not as if the game's fanbase would simply divide in half if it became multiplatform, a good chunk of new users would jump on board increasing overall sales. That's how it works with CoD.
CoD is an online game. There is always someone else to play with even if your friends don't own the console you bought the game on.
Up until MH4 the handheld Monster Hunter games didn't even have an online mode. They rely on people going to the equivalent of Street Pass Meetups and playing together. Some guy showing up with his Vita while everyone else has a 3DS is going to be like that Ridge Racer on PSP vs. Pictochat on DS picture.
Of course, Capcom has maybe inadvertently created separate unique brands for Monster Hunter on different platforms. There has been no Monster Hunter Portable releases on Nintendo, or Microsoft platforms. There has been no Monster Hunter Frontier releases on Nintendo, or Sony platforms. There hasn't been a Monster Hunter vanilla release on Sony, or Microsoft hardware since like 2005/2006 (whenever Dos came out, I'm too lazy to go look), and Monster Hunter Dynamic Hunting has been exclusive to iOS/Android platforms.
At one point I thought this may allow Capcom to sidestep the whole "My friend bought the game on 3DS, but I have a Vita" issue with creating unique releases for each platform. Since then though it's kind of become clear that in Capcom's quest to keep the largest third party franchise in Japan on the super cheap they just plan on there not being a difference between handheld and console entries. They'll just port the 3DS games, and call it a day.
Nintendo also published Rhythm Thief, that eventually went to iOS. I mean, it's not that all contracts are the same. The fact is that Nintendo is really pushing Monster Hunter in the West; investing in the online infrastructure and promoting it in Western territories is not something that you can do so easily without any guarantees.
Nintendo did all of this back in 2010 with Monster Hunter Tri, and then 7 months later Monster Hunter Portable 3rd came out on PSP.