If there is one thing that has stuck in the craw of many a Mega Man fan (well, there are several things, but that's beside the point), it's where Capcom suddenly decided to veer left instead of right following the events of Mega Man X5.
As many well know by now, 2001's Mega Man X5 was intended to be the end of the Mega Man X series. Thanks to Capcom going behind producer Keiji Inafune's back (perhaps showing how far back their enmity goes) to have a sequel on store shelves less than a year later, that would not turn out to be the case.
Whether or not that was for the best -- a question that firmly divides some fans, make no mistake -- the storyline of Dr. Wily finally taking an active part in the X series was continued into the next installment, then suddenly dropped afterwards with no cleanup involved whatsoever. Wily -- or at least his apparent proxies -- pretty much just up and vanished without a trace. In its place, the series took on a new storyline direction with the introduction of Axl and the New Generation Reploids.
GamesRadar includes this peculiar about-face in their list of six "Abandoned plotlines that would have changed everything," and explores that concept by looking at what could have been had it not been for whatever mysterious circumstances caused Capcom's developers to -- pardon the expression -- "give up the ghost."
That said, let's just suppose that Mega Man X5 was the end of that series. With no sign of the mad scientist in Mega Man Zero (and hence no apparent conflict between stories with regards to such), do you feel that the issue of Dr. Wily's revenge would have been sufficiently resolved? Or was more needed regardless?