Do polygon pours have to be either ground or supply voltage?
I've never designed a PCB where unconnected pour islands could not be got rid of (I've designed dozens and dozens, maybe 200 in many years) and I always connect a pour to ground if not needed for anything else. Consider re-routing some tracks to allow unconnected pours to naturally flood to each other. Copper balance is important. If copper balance is deemed not to be important and a pour is not needed then don't flood that layer but, in my experience, it is useful to have another ground plane. There will be exceptions of course.

Maybe show a small section of your PCB so that specific recommendations can be made.