I'm sorry, I admit I have not been following all the play test and such about this. However has "Class Building" been considered?
IE show how to build classes, consistently, then when people want to multi class use the class building rules to allow them to rewrite their class from that level on? This will allow a Multi CLassing fix AND keep compatibility with 3E, not to mention help in an even more detailed way with converting stuff back and forth between PF and 3E.
It can be done, I was even using a house rule derived from the materials in the 3E DMG to do so in the waning months of my 3E days. Only did it for 4 levels on two different PC's, but it sure looked very promising.