I think both approaches to terrain transitions have their benefits. RPGMaker's version may appear to handle one-tile wide rivers, but since it works by first splitting up the tiles in even smaller pieces and then recombining them, it is not immediately clear how this could be implemented nicely in Tiled. In addition, that system is very specific to RPGMaker and outside of RPGMaker I've seen the majority of tilesets with such transitions using the system upon which the Terrain Brush is based.
That said, there is an issue open about supporting the RPGMaker autotile format and maybe one day somebody will find a nice way to implement it.
Also, regardless of the autotile format, Tiled should of course enable the easy placement of fences, roads and rivers. I think the Wang Brush could be improved to enable this.