If you do allow two masters then I feel that the SS limit will be rough do to synergies with certain masters. If you have two masters with a limited SS pool then I feel as though it would more tough to make essentially two seperate crews, one for each master. I know within a faction the models have synergies with multiple masters, but i feel with a limited SS pool it would be hard to bring enough models for both masters.
In regards to having one master and a limited SS pool, I felt that it was fun to try and bring a list that would help you with all types of scenarios. I dont think that upgrades should go to the SS pool because upgrades vary greatly from master and faction (jack daw having 0ss upgrades for instance).