PyxelEdit as level editor - custom key/value data fields
Since PE uses a tile-able canvas as its painting area (key to its brilliance) it's also almost usable as a complete level editor for 2D games. Two things might do away with the need to use something like Tiled as a 'go-between' between art and code.
1) multiple canvases per doc, using a common tileset (for multiple levels, without having to manually sync the tileset all the time)
2) ability to add generic object data to tiles in a canvas, to tiles in a tileset, and to layers. Just key-value pairs, with keys and values being plain strings. Can be used for adding your own properties to tiles (invisible? glowing? foreground? background? etc), to canvas tiles (spawn point? goal tile? special action? etc), to layers (collision? in front of actors? parallax scroll plane? etc). In addition, (2b) a value type of "tile coordinate" in addition to "string" would make this perfect for connecting, for example, a button tile to a door tile.
Just dropping the thought – I realize this might take PE in a direction you're not interested in, and that these things might be 'not quite enough' to get rid of an in-between program anyway.