Zeref
(Despite his losses, his character was developed very well. Plus, he was a very interesting and intriguing villain even back when he was introduced in Tenrou.)
Acnologia
His Tenrou and Tartaros appearances were terrifiying, as should be of a villain. His Human design also looks very op and badass. Overall, he is a great villain(even if he doesn't have the deepest character). Too bad he didn't get a good fight...
Irene
A very interesting villain with a great backstory and development.