Brackentail and Frostfire were my favorites. I don't actually think of them as villains. They were both misunderstood. I also like Rockwing and Nightwing, they were both evil but I love evil characters because they are so interesting. The one villain I hate is Petalcloud. She is just heartless.
I don't really LIKE Frostfire. But I DO feel sorry for him, his dam was an evil villain, and he was handed over to the cruelest over-stallion in Anok. He was GREATLY mistreated by older pegasi. So all that cruelty forced down on him at such a young age likely hardened his heart toward... even his own family. Frostfire betrayed his nephew thinking he could save his mate and son. But of course, that never goes anywhere good. But I still think that he had a choice in trusting Star and helping him, and in being a good uncle. So I think it's partly Frostfire's own fault in the bad decisions he made.