I realize a lot of these are unnecessary immediately, so I compiled a list of suggestions that would be quick and easy to implement, yet very useful. Add more if you can think of any.
I was thinking of a Replace command. Let's say I build something and I want to be made out of BMTL instead of METL. I would select BMTL as my primary element and click on METL. It uses the floodfill script to search for all particles touching it of the same element and replaces it with BMTL.
Also, it's been said already, but flip selections and the ability to move selections any number of pixels (if a wall cannot be moved because it does not match the 4x4 grid, there could be an error message)