Since being cut from Brawl, many fans of the Super Smash Bros. series have rooted for Mewtwo to return to the roster of playable characters—in fact, he’s been ranked as the number one snub in our fan poll of most-wanted newcomers; and though Roy, another Melee cut wasn’t listed on the poll, he received a good deal of fanfare in the comments. Unfortunately, their inclusion in past Smash games doesn’t make it any likelier they’ll return.
Sakurai explains in this month’s Famitsu why Ice Climbers were cut from Smash, but he also reveals much more. Particularly, he mentions that it’s difficult to bring data over from Melee because the game is so old.
One of the major steps in developing each new Smash game is migrating data from the past installment to the new one, so the developers can save time from having to recreate every character from the ground up. Unfortunately, what this means is that if Sakurai were to bring back Mewtwo, the team would have to build the model, animations, and everything else as if he were an entirely new character.
The same is technically true of other Melee cuts, but given that they were all clones of other characters, they can be recreated with much greater ease than Mewtwo, who would have to be treated as if he were a newcomer.
The same information probably explains why all of the past stages in the two new Super Smash Bros. games are taken from Brawl, rather than re-introcuing popular stages from Melee and Smash 64.