Why not just get deeper uppers? I have four cabinets that are 15" deep and I wish they all were! I find those extra 3" add a significant amount of storage space...an extra row of glasses, room for wider dinner plates (12" and wider), etc.

If you go w/4" or more deeper, be careful about leaving enough work space in front of the upper cabinets...you don't want people bumping their heads on the cabinets while working nor do you want the cabinets to obscure the back of the counters. 3" will be OK, but any deeper may be an issue.

If you decided to go 4" or more deeper, consider also pulling your base cabinets out the same amount (or at least 3") to compensate. The big advantage with that is the extra counter & workspace...great! It does make a difference!

Check the specs on the microwave again and see if the frame really requires this. They're almost all that deep, but usually you can hang them from a 12" cabinet. It's just that the door is going to protrude beyond the line of the cabinets. If it's only the door I just wouldn't stress over it.

I forgot to say that often the only part that is really 16" deep is above the very top edge of the door where the vent protrudes the farthest.

I have deeper uppers on the wall with the microwave cabinet. The GE spacesaver microwave is the one I ordered for the for the cabinet.