It's an automatic registration process for eShop games, but it does only begin after you have linked your eShop account with your Club Nintendo account.
But no problem, just give a call to Nintendo's 1-800-255-3700 (6 am ~ 7 pm Pacific, everyday) Customer Service number, or use their webform to contact them, and one of the service representatives can manually register this and any other previous eShop content you might have downloaded.
And as to will Mewtwo be available any other way, I'm not sure, Nintendo hasn't made any announcement on if whether there will be or not, but just as a guess, it's always possible, as they did later release all the Hyrule Warriors pre-order costumes, so that we could all have a chance to purchase whichever ones we might not have been able to get.
So they might (no promises or guarantees) do the same and make it so everyone could also purchase Mewtwo for use in their games too.