Thanks for your honest feedback!
In Tiled 1.5, the "Terrain Brush" gets a big update and will support edge-based tile connections and blob tilesets in addition to the current corner-based terrain.
Templates indeed can't be used to place tile clusters (they're only for objects, and an object can only refer a single tile), but Tiled has a "Tile Stamps" view where you can save tile stamps for later reuse.
I'm always interested in making Tiled more intuitive and the documentation more clear, so your feedback is really appreciated.