You could render the 3D characters to a 2D sprite sheet, and then use the characters sprite sheets like normal. It is a tad more time consuming, but it might make development a little simpler.
You could also try to use a Viewport node and mix 2D and 3D together, but I have no idea if that would be difficult with an isometric perspective or not. The Godot demo repository has an example of rendering a 3D scene to a 2D scene.
Rendering the 3D characters unto a 2D sprite sheet is probably the most common way to get 3D looking characters onto a 2D isometric map, as then everything is 2D, which allows you to avoid some of the headaches of trying to sync a 3D scene with a 2D one. One of the issues I can see with using actual 3D characters is draw order, as isometric tiles in front of the character are (presumably) supposed to render in front of the character, which may be hard to calculate.
Though I have not tried rendering 3D characters on a 2D isometric map, so I am mostly speculating based on prior game development experience. There may be other ways of handling it, but that is what I would try if I was using 3D characters on a 2D isometric map :smile:
