Fluttershy is literally the perfect Eliza. It just works. I feel bad for  double casting Apple Bloom, but she has a small role so it's fine.

Twilight: Alex
Flutters: Eliza
Rarity: Angelica Church
Scootaloo: Phillip (Hamilton)
Apple Bloom: Angelica Hamilton
Discord: Phillip Schuyler
Big Mac: John Adams
Apple Family: Adams Family (ha, get it?)
Applejack: Madison
Spike: Jefferson
Sweetie: Peggy