The sprites are shaded, actually, but intersting that you thought it contrasted. You can sometimes see a shadow cut across one, which I think is a cool effect. I haven't seen it make them look flat. At one point the sprites also cast shadows, but that looked really bad when they were edge-on to the light source, plus the shadow often didn't connect with their feet, Otherwise, I thought enemies casting shadows looked nice, so I'd like to try adding it back, using a custom "shadow mesh" (turn the sprites towards the light rather than towards the camera to fix the edge-on problem).
Yes, I don't know that there's anything wrong with Godot's GUI features, but I just find it unintuitive because Control nodes are quite different to what I'm used to (the OHRRPGCE) and I need to unlearn!