Hopefully this will improve through the influation of AirFrance. Their seat-assignment scheme on domestic French routes is quite nice. If you have an ElitePlus (incl. KLM FD) card in your booking you are automatically seated in the first 5-6-7 rows. If you do not have the card in the booking you are stuck in the back. Not sure how they do two-people-in-the-same-PNR though.

A second thought; could it be that the system refuses to put PEs in a B/E seat initially? Hence prioritizing not giving someone a bad seat over seating someone next to their travel partner.