Ono stated that he would like to make a Nintendo X Capcom game.
Developers for Marvel vs. Capcom 3 had wanted to put a number of cameos from Breath of Fire in the game (Fou-lu from Breath of Fire IV was specifically mentioned), but this was eventually nixed as the Breath of Fire series was seen as "too Japanese for a game aimed at Americans". The planned appearances did eventually happen in the form of power-up cards for the "Heroes and Heralds" mode of Ultimate Marvel vs. Capcom 3, but to date Breath of Fire is one of two known Capcom series (the other being Power Stone) that have never made a full appearance in a "fighting" Capcom vs. game.
In the early 2000s (around the time Capcom lost the Marvel license) DC approached Capcom about doing a Justice League fighting game, which presumably could have eventually led to a DC vs. Capcom. Capcom was uninterested due to the perception that DC's non-Batman properties were floundering, as well as the power gap between DC's characters being much wider.
After the success of Capcom vs. SNK 2, Capcom were all stoked to go to make a third installment, having even started making sprites for the characters. But, at the time, SNK was going through bankruptcy and, since they didn't have the rights, they had to cancel. SNK made up for it with SVC Chaos once they managed to stabilize themselves.
that some of the rumours about Mortal Kombat vs. Street Fighter could have been true... if both Capcom or Midway decided who would have done the game. Midway's bankruptcy threw a wrench. Unfortunately, Capcom isn't exactly happy with the idea of Sub-Zero or Scorpion cutting Ryu or Ken's heads