It looks as though you’ll still be able to get Mewtwo in Super Smash Bros even if you don’t own both the Nintendo 3DS and Wii U versions of the game in Europe. Nintendo says that Mewtwo will available for purchase on the eShop as add-on content at a later date. Currently you need to purchase both the Wii U and Nintendo 3DS versions of Super Smash Bros to claim Mewtwo and the free bonus Smash Bros soundtrack which contains 72 tunes.
“The free download codes for Mewtwo will be distributed in spring 2015. The character will be made available to purchase as add-on content in the future.”