And while we're at it, since I don't see any mention of it yet, when replacing sprites, it's very important that they retain their collision polygons. I cannot count the number of times I've had to go and redo these when updating visuals.
Also, since this seems to be asset management wishlist time, I'd be keen on a reworking of the "Crop transparent edges" function. As it stands now, when cropping, you're essentially committing to those sprites (reimported images would come in at a larger size, and thus collision polys would never line up properly), but that's not always desirable. I'd love to see a checkbox or something to toggle automatically cropping transparent edges on export only (maybe per sprite, not overall - that'd murder export times), since the main reason behind trimming these edges is to ensure the exported spritesheets stay at a reasonable size.