It would seem unusual to have only one DLC character. If Mewtwo is free to all who have both game versions, that cuts down on the most intense Nintendo fans who would actually pay for him. There must be other incentives for DLC for Nintendo to make the big bucks.
Also, consider Mewtwo's release date. Spring. While games tend to be released in the fall and winter to coincide with the holiday shopping season, announcements for upcoming games are usually made in the spring and summer, what with E3 and the like. This would be a good time to release DLC for characters who will feature in the games that are announced in the spring, to create even more hype for those titles. Imagine how exciting that would be--a new Golden Sun game announced for 3DS, and Isaac for Smash DLC! A new, original Nintendo IP, and the main character can be downloaded in Smash right now!