I have seen a couple of alternatives: paste, adhesive application (not screened on) and then reflow. Then in the wave process use either a selective solder pallet or wave as is and take the rework for bad layout issues. Or another option is to assemble with paste on the solder side w/o adhesive and use a pin to paste for the through hole parts. Maybe even a solder doughnut with a gel flux for the through hole parts. Also tried once on a really bad design latex masking over all of the sm parts on the solder side. We had to use a lot of mask though so the parts inside the mask wouldn't partially reflow. It was pretty successful. Even programmed up an older adhesive dispenser to dispense the latex mask unto the PCB. Had to go back over some spots 5-6 times to get the right thickness of goo.