This is sort of a request for three features, which are related.
A tile property inspector (perhaps this already exists)
This would allow you to select a tile in the tile map editor and be able to A) see the properties of the tile, and B) edit those properties. With the current implementation, those properties would probably be the tile ID, and the H/V flip attributes. Editing the tile ID may not be as useful in this case, but I think it would be useful to be able to toggle H/V flip, without copying the tile and flipping it via keyboard shortcuts.
It might also be helpful to generalize tile properties, which would allow users to add arbitrary properties to tiles (which may not be rendered or displayed but could be output even if doing so requires a custom plugin).
Tile palette selection. The ability to assign a specific palette or palette offset to a tile. The main use case here is for tiles that use fewer than 256 colors (e.g. 16 colors). While the tiles could use subsets of the 256-color palette, if you have two tiles which you want in two 16-color subsets, you would need two different tile definitions as per the current implementation. For a more concrete example, consider a flower tile which uses 16 colors, you may want several variations, which use different 16 color subsets to change the flower color. If you want 16 of those variations, you would need to define 16 different tiles!
A potential solution, could be to have a list of namable 256 color palettes (to help users located them), and just select which one you want to apply to each tile via the tile property inspector (where the default palette is the one assigned from the tile set when the tile is imported or created).
Tile set locking. I know that the current tile-set editor has optimization features, however, it would be nice to be able to lock tiles in specific locations. This could be useful for retro systems where you want to keep certain tiles in the tile set (such as for text) but want to bank in / out certain tiles. It could also be used for a system that allows for more than 256 colors, which are accessed by extending a palette ID with the tile ID. Another feature that would be nice here, would be the ability to replace tile 0 with any tile (not just an empty one). A use case would be for the SNES Mode 7, where tile 0 could be used to fill the area outside of the main tile map after transformation.