I think they probably would have worked together very well.

Sonny would have been the Don, but Michael would have been the brains behind the operation, happy to go on with his public life as a pezzenovante.

I believe that Sonny knew he was not a good strategist, so he would have been willing to listen to Michael.

The only potential problem would be if Sonny refused to heed Michael's advice. But I don't know if Michael had enough fraternal love to sacrifice his own "legitimate" life to protect his family once Vito and Mama were gone.