Any argument saying that 1st party obscure characters got in so why can't 3rd party obscure characters get in is complete rubbish, as is the arguement that multiple 1st party characters from the same franchise got in so why can't multiple 3rd party characters from the same franchise get in.
There's a limit on the number of 3rd party characters that they're putting into the game so if they were to take a character from Sega it would be Sonic; no one else. That fills one space and I'm sure Nintendop would rather have characters from different companies and franchises (such as Megaman, Pacman, Rayman, Bomberman) than many characters from the one company and franchise.
Tails is by far my favourite Sonic character but I'd much rather Nintendo fill up the limited 3rd character spaces with the biggest names from multiple companies.
So in summary I'd rather see:
Snake
Sonic
Megaman
Bomberman
than
Snake
Sonic
Tails
Megaman
Even though I prefer Tails to all of the characters in that list (or any other company/franchise leading character).