4) A better density wizard, let's just copy coot and be done with it.
Ability to dynamically bind density levels or some other properties to
the scroll-wheel for that matter.
6) Integration/bundling of wxPython as an alternative to TCL/Tk??
Also +1. Warren mentioned this last year as a possibility for integrating PyMOL with the Phenix GUI, and in theory support for embedding a PyMOL view in wxPython is already present. However, that code appears to be very old and not maintained - I couldn't get it to work even after updating it to use the newer wx modules. I suspect there is not much work to do in order to resurrect it, but I don't know enough about PyMOL internals, or have time to learn. Note that this feature (if it were open-source) would allow anyone to make a native Mac PyMOL GUI and distribute that, so it isn't something I'd ask Schrodinger to subsidize. (If anyone else is interested in helping figure this out, however, let me know.)
7) Internal FFT routines to be able to read map-coefficients
+2. I believe the CCP4 libraries for this are open-source, so those are one option. CCTBX is another (I have tried this and it works), but this will be a lot more overhead.