Yep, Sombra was the most clever villain I ever met.
My villain is Tirek.
He's the first villain of all villains to be an actual SERIOUS THREAT to ALL OF EQUESTRIA. Despite being weak as an old man after he escaped, he manipulated freaking Discord, The master of Chaos and deception, like a fiddle.
He sucks the magic, talents and even the identity of ponies the same way Shang Tsung did to his victims. By the time he sucked the majority of Equestria dry, he banished Celestia, Luna and Cadance, and even backstabbed Discord once he was no longer useful to him.
He was also the first villain to put up a REAL FIGHT in the series after she absorbed the other three princesses magic and fought Twilight (after she absorbed all the Alicorn Magic) to a stalemate. The fight was ripped straight out of Dragon Ball Z and I jawdropped when I saw the fight.
Compared to Tirek, Nightmare Moon was mostly trying to slow the Mane 6 down at the start of the series and also attacked Celestia (who didn't fight back much until she had no choice), Discord was mostly being a troll and left himself wide open, Chrysalis may have defeated Celestia but then her confidence and arrogance got the better of her and left her wide open, and Sombra put effort in trying to win through setting up traps before he was banished, he would've won if it wasn't for Spike.
I also like the Dazzlings.