I've only tried to customize one fakie. It worked okay, it was good painting practice, but the plastic of the fakie interacted weirdly and changed the texture of the pony paint. The real MLPs don't do that. Also, the fakie plastic completely rejected superglue, which I've never had happen with MLPs.
Instead of starting with a fakie, I just got multiples of whatever pony was dirt cheap at the time. Back then, it was the blank G3 clone pony. These days, it might be one of the billions of G4 Pinkie Pies left on Target shelves!