OK, so I installed a little wiki for Avogadro:
http://avogadro.sf.net/wiki/TODO
I noticed in copying the Kalzium TODO list, that Avogadro fills a few
of them (exporting graphics, zoom, a separate app for clicking on CML
files in KDE… 
I’ll try to throw up a general design outline later this afternoon,
but since I’m hosting a visiting professor, life has been busy the
last few days. I’ll try to spin out the mouse tools to a plugin
system tonight.
Cheers,
-Geoff