I use hybrid picking a lot. Except for multi note lines on the same string. Starting with the pick or middle finger is for me determined by two things. Am I going from a low string to a higher or from a high string to a lower. I start with the pick for the former and the middle finger for the latter. It feels very natural for me that way. I guess the "rule" would be something like "use the finger that is closest to the note you are going to play."