I think Shimmer can be the second best or even THE BEST villain in all of the series. The reason? She did it all for herself.
While a lot of people think that Chrysalis is the second best, I think that she had some valid and heartwarming reasons for doing what she did (she had people to feed, so there's some sort of excuse for her behaviour). King Sombra is, sadly, underdeveloped (but if he comes back in season 4, prepare your hooves, because he has shown his capabilities as an outstanding villain!). Luna/Nightmare Moon was a good villain but she was used just to introduce a contrast to the magic of friendship and how being alone is not as powerful as it. Trixie is not exactly a villain (I think that the mane 6 made her the way she is), but she sure can be corrupted to become one.
Now,going back to Shimmer, she is truly evil at some point of the movie, showing that she was really capable to trick people to believe she wanted to be only "popular," when she was actually planning much, much more. A lot of people say that she's like an "Evil Twilight", but that's not what I think. Twilight was all alone before, but she always wanted to be a better student in order to be recognized. Shimmer just wanted to be praised, without even improving her magic skills.
The things that stops her from being the best is the fact that her potential was kind of wasted in EG, and that, even though she had great ideas, she's not as intelligent as Discord (the way he tricked every pony in both of the confrontations they had was just superb).
Anyway, I hope she appears again in the show. Right now, she's the third best for me.