I think that the biggest thing for me would be some sort of level sharing platform in game. Being able to view other's levels and compete in something, maybe time, maybe blocks used etc. would be really fun.
I also think that making every block output something no matter what could be interesting. Like, trying to shrink a white 1*1 with a black middle spot would give give a full black 1*1. Maybe the block that assembles pieces will also shrink them if necessary? You get the point, not giving out the raw input is cool. Because, once you laid down some rules on how things change and when, you allow these rules to be abused for unexpected puzzles. Inspired by that one portal level where you use that fact that the cube dispenser destroys the cube when activated to unpress a button
Also yeah, more colors could be fun, not sure how the inverter would work or how they would interact with each other, maybe by going around the color wheel?