I think Capcom is more willing than Nintendo, they have said that http://www.cubed3.com/news/15105/1/ono-nintendo-x-capcom-ask-sakurai.html, and the game would surely do well because Nintendo fans will buy a game with Mario, Link and Samus.
Fighting games are niche and it doesn't take a lot to sell more than your average Marvel vs game.
Look at this http://www.vgchartz.com/gamedb/?name=marvel+
Even on Wii U they couls easily sell much more than Marvel vs Capcom 2 for PS2 which had an install base of 150 millions.
I think Nintendo doesn't want it because it is a risk to Smash Bros, I imaine they probably want to have Smash Bros as the Nintendo 2D fighter, and Pokken fighters (if it exists) as the Nintendo 3D fighter.







