Not one to outright spill the beans, Seth popped in and opted to drop one last hint:
"To find my secret, you'll have to look further than you ever have before."
Ambiguous as usual, Seth.
However, some circles are convinced that single sentence holds some literal value. In other words, Mega Man 9's final secret rests in a background, perhaps as some sort of hidden image. Pure speculation, of course.
As a friendly reminder, Seth also provided three disclaimers intended to give the secret some context:
1) yes, "the secret" is real. Just because people looked hard and didn't find it doesn't mean it's not there. If you don't want to believe its there, that's cool with me (and probably a better use of your time).
2) the secret is not a huge deal. It's a footnote that would be included in an FAQ (even if it wasn't "the secret") but of you're looking for secret playable Wily, you'll be sorely disappointed.
3) in the case someone does find it and posts it to the thread, I will tell you "yep, that was it!" and we can cross a game off the list.