Goat eyes look more interesting, are used less often (and are therefore SPESHUL), and are, for some reason, really freaky looking. People keep forgetting that sheep and horses have those kinds of pupils, too; even more apt for a pony!
If you want something really strange, though, go for cuttlefish eyes. Their pupils are shaped like W's.
Goat eyes are more unique... and of course, being a Mary Sue means that she could have a rambling, incoherent backstory to explain why she and she alone possesses goat eyes. Perhaps being the last remaining descendant of a race of ultra-powerful half-goat-demon ponies from beyond the moon or something.
Have one goat eye, and the other a cat eye. Or better yet, your character is a mary-sue right ? The description of mary-sues tends to be less than constant. Just pick at random one or the other kind of eyes.