My understanding is that those coming from Unity often get tripped up by Godot's scene/instancing system because it's somewhat different than how prefabs work. Subtrees in a scene can be broken out into a separate scene and instanced. Elements as basic as a bullet should be implemented as a scene and then instanced and customized as needed. A common sentiment I've seen is, once it "clicks," they can't imagine going back.
I've only spent a few hours in Godot since recently cloning/building the master branch, and I already have a nice force-directed graph implemented. If it gets to a point where the number of graph nodes affects performance, I can move the force calculations from GDScript to cpp or another native option.
I haven't tried Godot yet but it looks really compelling. I sure wish they didn't make up a new language to script with though, there are already so many good choices. :/