I would love the ability to apply a manga screentone to a layer and then scrape off the parts that i don't want to keep like you can do when making real manga.
I know you plan to make layers moveable in 2.5. Maybe in 2.6 the layers can also be duplicated. imagine drawing a tree on a layer and instead of drawing the entire forest by hand you duplicate the one tree layer and place them around to make the forest.
These two features would give me even less reason to crack open other programs to finish stuff. Especially the second feature.