Yes. If I were going to develop a new Java UI (which is not currently on LOCI’s development roadmap), I would definitely start from ImageJFX, rather than starting from scratch. But it might be more impactful to develop a more general cross-language UI (see below).
I am not sure. While one of the original ImageJ2 project goals was to build a new UI, the needs of the community are very heterogeneous. The current UI is very flexible and meets many of the needs. Other more technical needs can be met by Jupyter Notebooks, or by embedding ImageJ into other more specialized applications (both Java and non-Java). I am skeptical of the added utility of a new JavaFX-based UI for ImageJ. I think it would be nice if it existed, but the development and maintenance costs of creating it are high.
In particular, I am not skeptical of the utility of new image viewers (written in Java or otherwise). Tools like the BigDataViewer and SciView are needed as we continue to move toward bigger and bigger data, and away from 2D slice analysis toward 3D and N-dimensional analysis.
I do not know where you are getting that idea, but ImageJ2 does indeed have a thorough separation of concerns, with functional layers completely separate from the aforementioned UIs. In SciJava, user interfaces are merely a type of plugin. That is why you can run ImageJ2 (but not ImageJ1) headless inside of a Jupyter notebook, for example. Or from a Python script. Or from a node.js project. Or as a RESTful image server.
Please develop a technical understanding of the ImageJ2 architecture before you speak about which goals have, or have not, been tackled.