With Marvel Vs. Capcom 3 already in the hands of some, footage of several characters' story mode endings have naturally made their way online. Tron and Zero's endings (viewable below) in particular are are quite interesting: Tron's contains the usual tongue-and-cheek MML humor we all know and love, while Zero's is -- well, let's just say it'll be raising a few eyebrows.
Neo Arcadia in 21XX? Well, we knew that was bound to happen eventually. The utopia's presence within the latter years of the X canon was largely hinted at in various sources, so it shouldn't come as a major surprise or a glaring canon error. If I'm not mistaken, this scenario would pen Zero to be from the pre to mid-Elf Wars era.
Not sure what to make of that "Mega Man Zero" remark, honestly.... meh. You can almost look at it as an in-joke: Capcom's making fun of themselves and the Mega Man series' cluttered continuity. Silly, at best.
(Thanks for the tip, Amir!)