Judging from the latest interview, Capcom head Keiji Inafune, had wanted to complete Mega Man Legends 3, but Capcom refused. Quoted from an interview from 4gamer.net.
“So, I told them that I was going to found my own independent company and leave Capcom. However, I stated that I was ready to make a contract with them so that I could keep working on those projects that I started. I couldn’t start making contracts with other publishers for sure if Capcom agreed to the proposition, but I wanted to see those projects that I started to completion. But it couldn’t be done. They answered, ‘We have no need to do that.”
“[I went to the trouble of]…Finding the right time, gathering the team members, planning strategies, all so we could barely start on Mega Man Legends 3. I really don’t want to quit at this crucial moment…but I can’t keep going at Capcom. I am too tired to keep going. I wanted to leave Capcom to recharge my energy, and support Capcom from there, but it seems they don’t allow it. I want to make all my effort to keep Legends 3 alive, but I’m really not sure I can do it.”
Via Game Blurb