1) Tile picker. In Tiled you can right-click + drag to select a group of tiles that have already been placed on the canvas. This is great for making patterns & arrangements of tiles to place elsewhere, and generally speeds up the whole process as you don't have to move the mouse all the way to the tilemap window and back all the time.
2) Set visibility of individual tiles. There are a few uses for this but in my case I need it for a Metroid style mini-map (tiles are revealed as you progress) and destructible terrain that regenerates over time.
3) It's been requested before but variables for individual tiles would be amazing. They can be used to define terrain types, animated tiles, and more. Currently you need a whole new tilemap object for each terrain type and all which isn't very practical.