Hi Marcin,
I did look into wxPython (Phoenix). It's not clear how well supported it is, since it seems like only one person is working on it. But there have been more recent updates on GitHub (
https://github.com/wxWidgets/Phoenix), so it's something I'm watching.
For the new GUI, a web app seemed too much of a jump currently. I do plan on more strictly following the Model-View-Controller design pattern so that we can potentially reuse code (e.g. for translating information from cctbx data structures for the View) if we move towards a web app.