Is anybody really surprised about this? This is how pretty much every major fan-made project goes. Somebody (or in this case, a team) pours their heart and soul into a labor or love. All the fans get excited and eager about it. At which point the franchise owner drops a C&D and shuts it down. I mean, what did everyone think was going to happen?
Mostly this happens because trademarks expire if not enforced. Somewhere in the bowels of Hasbro's legal department, a lawyer got worried that a legal case could be made that Hasbro doesn't have a solid trademark on MLP if such a game exists without being connected to Hasbro.
There's also the problem that Hasbro's licensing system is damaged or broken if fan works occupy the same space that a legitimately-licensed product would. Why would Capcom pay licensing fees to Hasbro for an MLP fighter (however unlikely it sounds) if Fighting is Magic exists without having to pay such fees and fans can get it for free? Capcom can't benefit in such a scenario and thus Hasbro won't get money. This really applies to all fan works.
The point that nobody seems to get is that fan works are a dead end. When I saw that a (highly simplified) city-management game had been made based around MLP, it gave me ideas. You could have Dwarf Fortress-style game where you are in charge of founding a new city of ponies. You could plan a railroad, there could be monster attacks, Changelings might kidnap your ponies and infiltrate your town, you could set up facilities for the Wonderbolts to put on shows, work to provide ponies with jobs related to their cutie marks, trade with other towns, and so much more. A skilled game maker could create a very impressive and entertaining game that would grossly overshadow what Gameloft put out. And be free. But Hasbro won't - can't - let that happen. Gameloft is a paying customer; they put in money to Hasbro to license the exclusive right to create their game. A fan work would be challenging that exclusivity and so must be dealt with.
The only way around I see right now is for fans to set up a kickstarter or something and buy licenses.