After Hasbro sent a Cease and Desist, Lauren Faust offered to design new characters for Mane 6. Why not just use the original versions Hasbro lost the rights to. Granted, they never lost the rights to Applejack, and changing Pinkie to a pegasus and Fluttershy to an earth pony would be non-trivial, but it still seems like it would work pretty well.
While a viable alternative, the fact remains that Mane6 has been given the Cease and Desist order by Hasbro and cannot do anything just yet without prior negotiations. That, and the series of events that occurred after the order have left Mane6 crippled by legal issues and staff leaves enough to halt any production.
That's still just as much a problem if they go with new ponies, isn't it?
Perhaps the characters aren't even going to be ponies.