Mega Man 6 is the only game in the series to be exclusively licensed to Nintendo.
The Japanese version of Mega Man/Rockman 6 had different music during the intro. If you've played the Mega Man Anniversary Collection or the Rockman Complete Works versions, you'll hear what I mean.
This is the only NES Mega Man game not released in Europe
Like Rockman 5 before it, Rockman 6 also has a manga adaptation, and like the manga for Rockman 5, follows along with the story of the game but ups the ante by having Rockman actually talk and interact with the Wily Robots! Also like the Rockman 5 manga, you can find the Rockman 6 manga under the BomBom manga label, and it seems to also have been penned by the same guy who penned the Rockman 5 manga.
For the most part, most of the Wily Robots/Robot Masters from Rockman 2 onward were designed by entries to Robot Design Contests held by Capcom. However, Rockman 6 had one that was a little different...
Capcom used to stick only to Japan for entries for the contests. When Rockman 6 was being designed, Nintendo of America decided to hold a design contest of their own, open to North America. Two American entries (Knight Man and Wind Man) were selected and used in the final game. All the rest are from Japanese designers.