I feel like if I were to do a "one fighter per 3P company" approach to a rebooted Smash roster, Capcom's pick would probably the be most affected by the direction of the roster. If you're going the COGH route, I would prioritize Ryu for hailing from the birth of the modern fighting game and generally being more relevant than Mega Man these days, but if you wanna do "Nintendo's All Stars", Mega Man would be more representative of that idea.
At least with other companies, you have an obvious character that can fit both slots; Sonic for Sega, Pac-Man for Namco, Steve for Microsoft (yes I'd prioritize Steve over Banjo even in a NAS situation)...