I like all the villains Nightmare Moon was cool and a good way to start the show/series that we all love. Discord was like a less crazy and evil Joker with magic powers and Queen Chrysalis just wanted to feed her swarm sure she almost killed everyone in Canterlot as a result but none of them were truly evil.
I know that Discord get's a lot of credit, but he really is great. He doesn't underestimate the Mane 6, and his design is rather well done. I also have huge respect for John de Lancie, not only for his voice acting work in MLP, but for his acting roles in Star Trek and Breaking Bad.
On another note though, I thought the Diamond Dogs were pretty funny as well, and I like fact that they are a nod to David Bowie.
I'd like to be a tree!
I have complete respect for several villians. Like Queen Chrysalis and Nightmare Moon. I love them. They are quite amazing ponies. Course I'm not sure if Changlings are ponies. Anyway, I love both of them.
Twitch a twitch! Twitch a Twitch.
If Discord had shown up on screen some more, I might have liked him better, but his introduction was quite rushed, and he didn't really appear many times in the episodes as himself, so it kind of ruined my perception of him. Also, he was pretty powerless when you think about it because all he did was use magic to spread a bit of chaos. I don't know why Celestia couldn't have handled him, seeing as how she could have easily beat Chrysalis under different conditions. And don't give me "she didn't have the elements", she has a giant beam of sun-rays, as well as Luna to back her up.
Anyhorse, antagonist wise, I loved Flim and Flam. Their design was ingenious, and the Super Speedy Cider Squeezy 6000 showed the evolution of pony culture between the seasons. Not to mention they had two of the best voice actors for the job with amazing singing voices. They were charming yet conniving at the same time. Trixie I liked the design of, but that's about it. Gilda is meh. Iron Will was kind of funny.
Chrysalis is by far the BEST villain. Not only did she sing amazingly alongside my favourite pony Princess Cadence, but she was so good that no-one even realised she was infiltrating the castle until Twilight miraculously escaped the caves with the princess. She actually defeated Celestia with the power of love, so damn she's got to be quite powerful in a world full of friendship. She's got a great insect design which isn't actually gross, but more evil and likeable. And she actually trapped the protagonists. I mean, Nightmare Moon, what the buck, she had the option to imprison Twilight and co way before they found the Elements but didn't. She was able to trap Celestia! And Discord practically made himself a walking target. He LITERALLY made himself a walking target at one point by giving them the option to find the Elements. He was cunning but ehhh. Chrysalis all the way really.