I can't tell if Godot's node system is perfect system for RTS. I definitely prefer it over the scene/prefab system, but not for a specific kind of game. For me an RTS needs a good terrain system, good pathfinding and fun-to-play AI. Godot has some pathfinding included. No terrain node, but you can still design it in a modeling software, or generate it procedurally with a script or C++. AI depends on how your game works.
Oh and also you would need solid networking if you aim at multiplayer. This is intrinsicly hard whatever engine is in use. Godot has basic networking classes, and a more high-level, rpc/master/slave system will be available in 3.0.
GDScript is really easy to learn and just works™. It is nicely integrated in the editor, and can actually be debugged. The only thing not to expect is blazing fast performance, for which you can still use C++. And if you want a compromise, C# support is coming, for some time in 2017.
You'll be surprised that the current documentation of GDScript is more or less the reflection of Godot's C++ classes oriented for scripting. There is more under the hood of course (some of it is explained here http://docs.godotengine.org/en/stable/reference/_developing.html), but for gameplay code with nodes it's simple enough once you get it (assuming you have C++ experience already), I can run/debug with QtCreator without too much hassle. Just expect it to be more tedious to write than GDScript at times, because, well, it's C++^^
And if documentation is really lacking on unexposed C++ classes, you can still ask the community :)
You are right about the fact switching to another engine is a bad idea when you already got your hands with one. It's fine to get experience on another tech, it's mostly your choice I would say. Are you happy with Unity? I did the switch myself after the massive 2D update and litterally ported my Unity project and still sticking with it, because the engine fits my needs for that project, I like the workflow and FLOSSyness of it. 3D is a bit meh at the moment but will get a major update too in the next months.