On that note, I think that Batman's favorite pony would probably be Twilight Sparkle--influential, smart, and looks really cool in a black, skintight costume.
Alternate Hunchback casting:
Clopin: Pinkie Pie
Quasimodo: Twilight Sparkle
Phoebus: Gosh dang, he's hard to cast. Rainbow Dash? Extra irony for Clopin attempting to kill both Quasi and Phoebus.. (Cupcakes, anyone?)
Victor, Hugo, and Laverne: the Cutie Mark Crusaders
We still have incest between Celestia and Luna, but I don't know how that can be easily avoided.