User blog comment:Tails1/Is Sonic's Future with Nintendo trouble??/@comment-3027069-20130518131135

There is still the possibility of seeing Sonic on other consoles. The agreement only states that Sega will work closely on Nintendo for these three games.

Personally, I do not mind the team up, especially if it improves the quality of the games, the fun value of the games and draws new fans to the games. I believe this will be beneficial in the long run for both Nintendo and Sonic. In fact "the long run" is probably why the did this in the first place.