I wish that if I joined a mission requiring perks that a message stating "You do not have the required perks" would pop up. This could be the same message we see in the hangar. In addition perhaps "freeze" the required mission perks once joined so as to not to incur any unpleasant surprises.
This would solve currently only a minor annoyance of being left behind when a mission rolls, but it may also serve a larger role for future inclusions...like perks being used for ordinance loadout for example.