I can only guess it is the experience. If you watch my first gifs, the timing was far from being perfect, while if you watch the gifs that came after Fate/stay night (when I'll post them), I believe that a slow improvement can be seen, at least to my eyes
I can only suggest to download the gifs that you deem as "well timed" and to check their times, to have a wider answer.
What do you mean by "perfect". Is it the cropping? A normal rule that I use is to crop in a way that the character's eyes are always at the center of the picture.
If the character moves his head, then the eyes have to be centered on the frame when he's looking the camera (a frame which I usually set with the highest timing).
If it's an action gif (meaning that they spin all around), usually cropping in the middle will do. If not, manually adjust it as your eye suggests.
Not sure if I got your question right, but at least, those are the simplest tips I could give