I never got around to making an official list of my favourite directors, but were I to do that now, it would likely look something like this (in no particular order):
Paul Thomas Anderson
The Coen Brothers
Let's break it down.
They all have multiple movies in my Top 100, except JM who only has one, but most of his other movies are dark green for me. Also, his one movie is All About Eve, so suck it, everyone else. By memory, AK has 3, HM 4, PTA 3 and the Coens 2 or 3. Out of the five directors, 4 have one movie in my Top 10. I've seen all or most of their filmographies, except JM and AK, and it's all mostly green, with the odd orange laying around.
PTA's weakest movie is Hard Eight, which was his debut. I must rewatch The Master sometime because it didn't do much for me but I couldn't explain why. There are a few Coen movies that I have trouble connecting with, notably their more personnal, Jewish efforts like A Most Serious Man. I mostly love them when they're making comedies but they sometimes fall flat. I rewatched Burn After Reading recently and it was mediocre compared to the rest of their work. I wouldn't call any of it terrible. I haven't seen a single mediocre Mankiewicz but I need to watch many more and I've avoided the Kurosawas that are not widely hailed as masterpieces, which is why I can like everything there.
I would point out that they're all writer/directors (JM not always) and singularly proficient in their craft. The Coens are among the best writers of dialogue and screenplays of their age and Miyazaki is probably the best animation direction of all time. They've all mastered the art of making movies, from the editing to camera placement. They're also excellent at casting and directing their actors. Kurosawa/Mifune and PTA/PSH are some of the best director-actor collaborations of all time, and I am not even going to mention the Coens regulars.