Well, chances are that we'll be able to install it via .cia file, as has been stated in this thread. I'm willing to just buy it through the eShop if the price is reasonable, though. Likely Mewtwo is just a reskinned Lucario for the most part, so anything more than $10 would be ridiculous.
The Mewtwo character itself will be delivered via an update for everyone, of course. The DLC will just unlock it as a playable character.