Ryu doesn't make sense, at all... without any context, that is. However, if we knew the context, it might make sense. The fact of the matter is... this is ONE HUNDRED PERCENT TRUE. Ryu and Roy have data in the patch, this has been confirmed by multiple sources. Deny it all you wish, but its legit.
Ryu does not make sense on his own, hence why Nintendo must have gotten something in return. I doubt Nintendo would've agreed to allow Mega Man in only if they added Ryu later. Sorry, I fully disagree with this theory.
If anything, Nintendo is either A.) having Capcom make a new game for them (probably related to Street Fighter; a Nintendo vs. Capcom game would be a neat thing to see),
or B.) Nintendo bought something from Capcom, perhaps the rights to an IP. Capcom only agreed to it if they got another character in Smash Bros. This would make sense if, maybe, they bought the rights to Mega Man (Capcom isn't doing anything with it) so now there's no "Capcom" character in Smash anymore, so Capcom requested Ryu as part of the deal.
B.) isn't all too likely, but if Capcom is as strapped for cash as they appear to be, they might've considered selling an IP they don't care about anymore but Nintendo would. Regardless, A.) is probably more likely. Smash Bros. isn't a traditional fighting game; just like with Street Fighter V, Nintendo might've commissioned Capcom to develop a traditional fighting game on Nintendo platforms, to try and get some of that traditional fighting game audience to Wii U. There's not many fighting games on Wii U at this point. In order to help promote it Nintendo agreed to add Ryu to Smash as well.