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Hmm, I see what you mean, and while this would fix some of my workload, it would not fix all of it... On the title screen surface layer, that would have helped out greatly, as they simply repeat now and again, but those are only with standard tiles and larger background pieces which repeat. There are some objects that are simply just too big, and don't repeat enough to warrant an entire tile reconfiguration. Take Kraid, for instance. He has quite the complicated model, but his parts never repeat themselves in the game after that point, so the tile solution would just cause more work for me in the first place. Really, a replace tool would kill both of these issues at once, by allowing just two clicks to get rid of an entire sprite layer/color.

Completely agreed! There we have two different issues, both needs to be improved :)