How to choose who flies with and how to set skill levels without it being random

Under options, you can check "Squadron Management" and then in the Squadron Editor Panel you can assign who flies with who (but only in your squadron), by swapping the position of one pilot with the other.  Just click on the one pilot you want to swap with the other.  Each set of four pilots is a flight: flight leader, wingman, leader, wingman.

You can also change the skill of the squadron with the "SKILL" drop down on the  Squadron Editor Panel.  The value chosen is the base skill of the squadron, but individual pilots with more experience will be higher and individuals with little or no experience will be one step lower.  (It's not random.)  

If you want to change the experience of any pilot, just double click on their name and you can give them more (or less) missions and/or kills.