Why doesn't the Terrains system just work similarly to RPGMaker's autotiles? It's far superior and gives much more control. I've already gone to the trouble of making my tilesets compatible with that method.
I really like Tiled, but the issue is that it lacks options. The way it's set up, I have to insert tiles 3x3 at a time, or 2x2 at a time, or if I want to have a 1 tile wide river, I have to do that manually, because Tiled wouldn't know what to do if I tried. However, with RPGMaker, it absolutely is equipped to handle it.
My suggestion is to add a brush style mechanic so users can choose to have a 1 tile wide option as well as the 2x2 and the 3x3.