I'm heavily leaning towards buying the New 3DS because of the hardware refinements and expanded library of games led by Xenoblade Chronicles. I'm a big fan of the handheld, so I don't think I'd stay behind as it evolves.
I haven't played in a while & I only just downloaded the new PC client. But from what little I dabbled in before, creating an account will net you a handful of starter decks & winning games against the AI challengers can net you some new cards with which you can customise your decks. All that is available for free along with PvP.
As I understand it though you can buy physical decks & boosters, which come with a code that you can use to unlock the cards in your online collection. I'm not sure if you can choose to buy online stuff only or not- I would think you could, but again I've only really dabbled in the free to play side of things. Davoid can probably elaborate more.