Well, I guess that you could go
Darker and Edgier on the whole concept. Like, I dunno, have the horses be living in this kind of weird horrible regime under the control of some bizarre Wicked Witch who forces them to be continually happy and everything. The series can then be about rebellion and control, challenging the idea from fairy tails about happy ever after and utopias, growing up and coming to terms with the world as a much less friendly place than you would-...
No, that still sounds pretty awful.
Yeah, I can't think of any good new angle to give to it.
(OOC: Neither a brony nor a non-brony, as I don't have any feelings one way or the other on the subject and have never even watched the show, but I can't help but be amused that this is a subject that has managed to generate so much controversy

).