Personally, I find the whole "Alternate Universes" thing a bit immature. (no offense) True, there could be such universes, but I find it illogical to think that one would be comprised of works of fiction. Secondly as to yoshi mastar's thoery of Mario telling Miyamoto, even with the technology that some various places in the Musroom Kingdom, heck, World have (eg. X-Nauts, Smithy, etc. ) I have never seen anyone in Mario's universe come up with anything more advanced than a time machine (and I consider that non-canon.)
Here's my theory....
The entire universe where Mario co-exists with the Earth is non-canon, since Nintendo never specified WHERE the Mushroom World is. The Mushroom World exists in a universe (not parallel mind you) where the Mushroom World IS our Earth. Brooklyn does not exist, but if I am correct, Nintendo never said Mario was from Brooklyn, it was third-party companies that did. All humans are "born" via storks, which is confirmed further with the onset of Yoshi's Island 2, with Peach coming form the stork. Mario & Luigi were raised by a small colony of humans living in an obscure location in the Mushroom World. In fact, one might even theorize that ALL real world objects were carried by the storks. We do not exist in Mario's world.
This, however, contrasts stories in manuals of other Nintendo games, eg. Starfox, Metroid, F-Zero, etc, which state that they take place in our universe, in a different time or location. Starfox is from the center of our galaxy, F-Zero and Metroid are from the future.
Super Smash Brothers is a clash of trophies, brought to life by a child's imagination. In BOTH games. (although in the first game it was dolls)
Although I think we all agree it would be cool if the Mario universe co-existed with ours, I think we can safely say it doesn't so get over it.
.....So sums up my theory.
I think about this way too much. :D
AND GET OVER IT PEOPLE IT'S A GAME!!!!!
:)