The Chase - Though it starts as what seems to be a shipping fic between an OC and Derpy (
and it is), it's actually fairly interesting. Personally, I feel it gives a bit too much weight to biology, but IMO, it does a good job of making the differences between the various races significant and meaningful.
edit: removed the link. Just realized that it had a sex tag, which it seems to be inching towards around chapter 20+ and I don't feel like getting in trouble (
it's mostly insinuations as of chapter 21). Nothing as of yet, but I'm going to hedge on the safe side. You can look it up on Fimfiction yourself.
Adding this:
Winning and the Pitfalls Therein - Quoting the summary seems best:
"What if the villains were allowed to win without a fight? Would all of their plans bear them the fruits they so desired?
Probably not, especially when their royal adviser is Twilight Sparkle."