I didn't really have an issue with queueing at controls. They are very much geared up to get randonneur-friendly food out quickly. But managing your time at controls is vital. Take your empty bottles into the controls and fill them while you're in there. I usually bought a large bottle of water and filled the bottles while eating. If you're going to add or take off layers do this while you're eating. I had a small bag within my luggage that I carried in and out of controls that had toothbrush, sudocrem, wipes, ibuprofen, contact lenses, glasses, etc so I always had the things I might need to use whilst in there.
Also, don't be afraid to leave your mates behind if they're faffing. They will forgive you and you will see each other on the road.