Actually the two cases are VERY different.
SEGA's big meal ticket is Sonic, all of the other top SEGA franchises absolutely pale in comparison to it. They have some other franchises that are important to SEGA themselves, like Jet Set Radio, Space Channel 5, Golden Axe, NiGHTS, Samba De Amigo, Monkey Ball and Streets of Rage but none of these franchises are iconic to gaming as a whole, and especially not to Nintendo. All of SEGA's eggs are in the Sonic basket. Eggman is a VERY iconic villain, one of the most iconic villains of all time, and Tails is like THE sidekick. He's Luigi.
Conversely, Capcom has at least 3 very, very iconic franchises, each with a very clear mascot. Mega Man and Ryu, and then Leon (as well as Chris and Jill) for Resident Evil.
Mega Man and Ryu are more iconic than any of the other characters that aren't Mega Man or Ryu in their respective franchises. Protoman doesn't hold a candle to Ryu, and Guile doesn't hold a candle to Mega Man.
I already got Snake and Bomberman done!
You could easily argue that Sonic is a much bigger franchise than Street Fighter or Mega Man, and is so intimately linked with Mario itself that it could get more than one character.
There's no such thing as "unfairness" when it comes to 3rd Party representation. Capcom have more franchises that have made a bigger impact than SEGA or Namco, but the one franchise that SEGA has that made an impact made a bigger one than the Capcom ones.