Even funnier if you think about it because in Japan, they both have the same exact name.
Word of God: According to LowBrow Studios, Dr. Wily did survive in "The Battle: Part 2" (The Season 2 Finale of Sonic for Hire, where Mario summoned a bunch of villains, including Wily to go after Sonic. Almost all of them got killed though) but he had "one hell of a head injury".
As for Sonic for Hire, they too have a Facebook page with some of the posts being typed as if Mega Man was saying them. It's not updated as often as its sister series though.
According to the Facebook page, they had no idea who Nappa was. When Guts Man becomes a ghost and follows Mega Man around, a lot of fans thought it was a rip-off of Nappa. And in the trailer that depicts the series finale, they're both in a car, listening to Ghostbusters on the radio, a theme song that Nappa completely took to.
They both seem to be different, as Guts Man shows Mega Man a bunch of flashbacks of his life in an effort to better help Mega Man.