Those reasons are, erm, unknown, but you can bet that they're various. The game was centered around user-made content from levels to characters.
It would have let fans play as other Capcom notables beside those in the Mega Man roster. Perhaps it's because Keiji Inafune, creator of the series, has left Capcom to go elsewhere. In 2010 Inafune-san said it would "unite all Mega Man fans together in one place".
Well Mega Man fans can now at least be united in disappointment, or perhaps joy? Fortunately the gaming big shot Inafune did teasingly add before his departure from Capcom that "there are other things going on with Mega Man." Well that's okay then.
Are you feeling down that Mega Man Universe has imploded?