Yeah, I agree. There's a lot of great things about Unity, but there's also something lost in flexibility and maintainability (when you own your structure). I taught a college course in Unity and it was interesting to see how students' coding skills/knowledge and the Unity editor interacted.
The end goal for Pixel Proof is to make good pixel art easy. I'm making tools that other pixel editors can't do, implementing all the basic necessities, and keeping the interface simple. Layers and animation are the biggest features left. A type of index painting is implemented already, but not exposed. Then there are a bunch of interface changes I have planned (toolbars for tools and palette will be next).