Do recall people that Sega more so than Capcom is a HUGE part of Nintendo's history. First as a rival and second as a partner in crime.
Tails, Knuckles, and Robotnik are as recognizable of video game characters as Luigi, Peach, and Bowser. There's nothing to say that Sakurai wouldn't view them as special cases of video game and as such Nintendo history.
1. Comparing Luigi, Peach, and Bowser to Tails, Knuckles, and Robotnik in the sense of being iconic is understandable, but to be included in a game bringing together Nintendo's all stars is a completely different story.. Luigi, Peach, and Bowser are all in because they are the mainstays of Nintendo's most well known and influential series. This same logic would apply to their Sega counterparts, if this was a Sega crossover game, not a Nintendo one.
2. It is obvious that Sega is a huge part of Nintendo's history. However, that doesn't necessarily mean that they deserve a 2nd character. Sakurai himself has stated that Namco, the team developing the game, will not get special priority over other third party companies, for having characters in the game (meaning that they for example won't get 2 characters just because they are helping develop the game). Now if Namco, the devs of the game, don't get 2 characters in the game, why would Sega? Sure, they have history and have been in good terms for years, but that should only be enough to justify Sonic in the game alone. Nintendo IP's have many characters per franchise because they are important first party Nintendo characters, so they belong in a Nintendo all stars game. Sonic, along with Mega Man, Snake, or any other third party character, is there as a guest character, representing not only their franchise, but their whole company's relevancy and history with Nintendo alone, deeming a second character unnecessary.
3. Can you imagine the ****storm from the fans if a second Sonic character got in, but not a second Mega Man or Metal Gear character. (Or even worse, a first party fan favorite not making the cut)