It would be nice if tilesets were not a 1 dimentional list of items that gets put into rows, but rather a static square where you can move tiles around. The way it is set up currently, it's very hard to move tiles around, and if you want tiles to be connected in a meaningful way, you have to add a bunch of blank spacer tiles (see below). And if you need to move anything, it's a disaster.
Spacer tiles:

After that's done, we really need a stamp tool, where you can select multiple tiles to place at once. Tiled handles this well, you can see an example here:

You drag to select tiles in the tileset, then when you go to place them, it places them as a group. Saves a lot of time. (This isn't the best example of usage, usually it's a house or tree that takes up multiple tiles)