You'd have some ancient backstory probably involving Ironhoof Celestia introducing Unicorns to a more powerful form of magic(That just happens to slowly destroy the world around them) and expanding Equestrian rule across the world, driving the unwanted creatures into obscurity (And subjugating those that remained) and using these powers to sieze control of the elements and weather patterns themselves.
Eventually the Unicorns betray Ironhoof Celestia, Imprisoning her in the void. They become Alicorns themselves (Read - Sorcerer Kings) and divide the ruins of Equestria up between them. The leader of the group of Unicorn-Betrayers, in order to complete the seal on Celestia's prison, takes the transformation a step further and becomes the Draconequis (of Tyr. Replace with appropriate ponyplace).
I figure you'd have Unicorns as the Templar equivalent, Earth ponies as an oppressed underclass (somewhere between non-templar humans and Muls, used for labour, gladatioral entertainment etc), and the Pegasi as either rare survivors (hated and feared desert dwellers) or something similar.
I'm sure I could figure out some idea of what species fit what role in Dark Sun Equestria, but I'm sure you get the idea. One of Dark Sun's themes is subverting the usual roles of the races involved, so it'd all be keyed to that concept and the ruined world. Oh and everypony gets a psionic trick or two.
It could be an entertaining thing, but would require a lot of work to figure out the setting.
Alternate, mildly more depressing concept;
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The Rajaat analogue could instead be Twilight Sparkle. She's so powerful magically because of her research, that will eventualy become "Defiling" magic, with Celestia and Luna being overthrown at some point during the ponified cleansing wars.