I'd love it if you could reorder/sort tiles and sprites. Something that's coming up often is I'll make some basic tile (bricks, for example), and then later make a variant of it (say, bricks with a crack). But since I'll have made a bunch of other tiles in the meantime, they'll be pretty far apart in the list of drawings. If I could reorder that list, it would make it a lot easier to find related tiles.
Same goes for rooms/palettes. I like to have my rooms in the order the player will enter them, and if I add a room that transitions between two existing ones, it'll be stuck at the end of the list, instead of in between the two it connects to.