In a FAQ on Capcom-Unity, Capcom denied that Keiji Inafune's departure had anything to do with the cessation of his pet project. "Unfortunately it was not felt that the Mega Man Legends 3 Project met the required criteria" to go into full production, and thus the plug was pulled. Our guess is that Capcom is backing off from the 3DS after it didn't achieve stratospheric sales immediately.
This news comes immediately after the start of a fan campaign in support of the continued development of Mega Man Legends 3. Combine that with the already beleaguered nature of Mega Man Legends fans who had to wait over ten years for news of a sequel, and, well, there's going to be a giant Servbot-shaped shadow cast over any announcements Capcom makes at Comic-Con this week.