According to the rumor, Mewtwo will be bought at the eshop this June. Unfortunately, my brother and I bought our own copies of Smash for 3DS, so one of us is going to get the Mewtwo DLC for free, while the other has to buy it later.
Yes, I've played Project M before, but that was before they added Mewtwo and Roy into the roster, so I don't know how much the mechanics has changed since.