To quote eishiya from the Tiled forum:

When highlighting a layer, have an option for a light colour as the fade colour. The dark default doesn’t work well with dark tiles, as they blend in.

Could probably be added alongside the grid color configuration.

On the Wild Pokémon tab, show the total encounter rate and level range of a given species across all slots mapped to them. This would help to visualize encounter chances.

Add an option when right clicking a directory in file view to tick/untick the whole directory.