I know, I know, necro-posting, but MM25 had a bit of new info on this one (see second quote-bit below)
We, the fanbase, decided that the X6 Zero ending did not have to happen immediately following X6, in order to validate the X-series titles that follow. There is no official word whatsoever on how exactly those titles relate to Rockman Zero. Whether they were developed with that premise in mind, or follow a different ending to X6, these titles do nothing to mess up continuity.
I suppose it technically is an assumption but it is a logical one. It's a known fact that MMZ was in development already when X6 was out and that Inafune's initial reaction was that it'd be trouble for storytelling. And while it was odd that nothing specifically indicates Zero's X6 ending as being a "sneek peek" at anything, it is equally odd that no event within the rest of X6 ties into it, including X's "good" ending where Zero is present and accounted for. It's only because of the MMZ Collection website that the Nightmare Incident relates to Zero's sealing/research at all, as X6 itself doesn't specify what Zero is hoping to accomplish.
Either way, Inticreates has only given us the statement that X1 to X6 is "1XX years ago" and that classic is "more than 200", with Zero being studied for "50 years." As the X-series spans no more than a few years up to that point, we have decades of leeway that only XCM could even begin to stress.
Since the last thread post in 2010 there is a new sliver of information on this front. Higurashi (lead artist on Command Mission) was asked about Command Mission's place in the timeline in the MM25 interviews, and here's what he had to say:"Command Mission" is technically a spin-off, so even though it takes place in 22XX, it's not necessarily the same "22XX" during which the "Zero" series takes place. Still, we didn't want to cut it off completely just because it's a spin-off. Our goal was to incorporate some of the "Zero" series' flavor in order to make it feel like "Command Mission" is still connected to the other games, like it is a part of the same family. So it might be easier if you regard "Command Mission" not as "a story that takes place between X7 and the Zero series", but rather as "one of many potential futures that exists independently from the Zero series."
I've said it before, and Inti basically admitted it themselves in MMZOCW, but I'll say it again: The lack of "22XX" references from Z2 onward is much more justly laid at Inticreates' feet, what with the Dark Elf's origins and such, than it is at any notion of trying to make room for the later X-series titles.
Command Mission is a squeeze, but I don't think there's any reason it NEEDS to be an alternate. It would seem that idea is still on the table within Capcom, though.
This makes me all the more disappointed about Mega Man Online's cancellation. Even if everyone is a Copy Chip clone and even if the game would wind up being non-canon anyway, Cinnamon's visions of Neo Arcadia are the only effort ever made to actually reconcile elements of Command Mission and Zero series. It would have been an interesting point of discussion, for sure.
The only word of their activity prior to being sealed is the Shining Arms, which we can just presume were wielded by X, or are the epitome of Neo Arcadia propaganda.
Any particular reason Zero isn't just as viable? If the later-X-series games and the Zero series have one thing in common, it's that the whole multiple-primary-weapons shpiel kinda became Zero's thing. One could draw parallels between Dark Cross and Shield Boomerang, and the Frost Javelin and Triple Rod maybe.