It looks like Shards of Equestria has been hit by those crazy lawyers over at Hasbro's legal department. As is the norm, they are required to protect their property by US law, but the specifics of the cease and desist have not yet been released. Keep an eye on the dev blog for information on what exactly is going to go down.
I guess we need to build our own card game from scratch? MTG is a great template, but I'm sure we can think of something new! Get on it smart people!