I can see what you mean. However, We are also forgetting tho the possibility of extra dlc packs emerging for the others as well. Even with Sonic and Megaman in the game, similar agreements could be made with the other companies to get more in.. (Like Tails and Knuckles to accompany Sonic, for example. (Dunno about Pac-man.. only thing I could think off on that end would be Mrs. Pacman, and she seems more like she would be clone material..)
All of this was also before the concept of such DLC was even considered for Smash as well.. Sakurai probably didn't even take any of that into account before the whole Ray leak fiasco, and... what ever Iwata and Sakurai probably talked about in that meeting they had.. where they discussed that smash ballot to begin with. It probably would have taken awhile for Sakurai to be convinced that the DLC packs could be worth it... (and the ray fans have shown it most certainly would be)
I mean, getting in smash in general is one thing, as it seems like a fairly simple matter. But in terms of Paid DLC, its an entire different ballgame.. The possibilities for agreements are much easier, since the packs would be purchased multiple times, generating profits for both parties..
Edit: Just to add to this, it also gives Nintendo to have another method of getting profit for the game, even further into it's lifetime..