@Machomuu: The issue is that Capcom's explanation is superficial and utterly devoid of actual meaning.
Two canonities being contained in a larger meta-canonity does not change the canonities and it does not make them one canonity. If you take a jar of peanut butter and a jar of jelly and put them in a bag, they are still as separate as they were before. The multiverse canonity /only applies/ to the multiverse, not the RPs within it. >_<;
...and there are no games or official content that takes place in the multiverse, so it means nothing. @_@
Do you see what I'm saying? =/
On the contrary, the multiverse applies to any supposition. Any at all, there are infinite multiverses. Say I were not to write this message, that would create a new universe. Say I were to word this sentence differently, that's a new universe to. Heck, say I were to write this post slower, new universe. As I said, several times in fact, there are multiple canons (similar to what you said), however, the difference between this and, say, Final Fantasy (the anthologies, not the related ones), is that there was a point where Megaman Classic and Megaman BN were only one canon. When was this? Before the internet revolutionized the world. Or, on the other hand, before robots did. So really, it does make sense, there was an action somewhere in the history that caused the universe to split into two separate universes (canons), the BN one and the Classic one (one where the internet has become a major part of life and one where robots have, respectively).
And actually there are games that take place in a multiverse. Many of the Dragon Ball games take place in an alternate timeline or universe than the "Main Timeline". Also, for a more relevant example, take Pokemon. Ash Ketchum, Red, and Red (Adventures), all take place in different universes, but what's unique about these is that they are all different versions of the same person (counterparts, if you will), but at the same time they're not the same person. Similar deal (Though still different in a few ways) with BN and Classic, the Protoman of Classic isn't the same person (well, he's not really a person at all) as the Protoman in BN, but he is his counterpart, and vice versa. I freakin' love multiverse and timelines, such a theory of infinite multiplicity that can apply to everything, and it's so simple yet so complex at the same time. /Gush
Also, I never said they were contained in a larger meta-canon, they're not. The only way that is possible is if somewhere in between there is someone who crosses over into the other universe, thus reconnecting the two universes without them actually converging (if they were to converge, it would become a single canon once again, that's pretty much the only way there could ever be a single...well, that's not true; by converging there are technically more universes created, but as far as the games are concerned, that's the only way they would be one canon again as far as our universe (in the real world) is concerned).
Anyway, it's not really appropriate to continue this- here at least, I'd love to continue it in another section, though. But this is fun, definitely a good use of time (no pun intended).