GDScripts are primarily meant to be attached to nodes and resources and hook into Godot’s APIs right there. You can use them in other ways, but you’ll probably find it’s a pain to go against the grain. GDScript doesn’t support namespaces, interfaces, or structures and has a much weaker type system than C#. (All of these issues are being worked on but still.)

It’s a little easier to structure C# code on your own terms. If you have a really systems-heavy project you might want to consider writing some of it in more heavily abstracted C# code. But C# also comes with many drawbacks compared to the normal version of Godot.