Now that 4.1 is here and there are no changes to the material profile system, I would like to bring this back into picture:
Look at Slic3r's profile system, it has everything needed to properly manage materials, and there is no reason to not have that wonderful ability in Simplify3D.
Please, please, please consider when working on future updates, it's been far to long without any real improvement in this area. I'm getting tired of modifying my FFF files to get some sort of material control back.
If the main consideration is to maintain interface continuity, maybe consider having the legacy version along with a new profile management system.
Hoping this gets some traction this go-around.