Better yet, I would say, would be to include the complete version number in all of the various paths, i.e. /usr/bin/ion-2.whatever, with the symbolic links /usr/bin/ion-2 and /usr/bin/ion, and share/config files can go in /usr/share/ion-2.whatever/*, /etc/X11/ion-2.whatever/. This would allow for any number of different versions to be installed simultaneously, which IMHO, makes more sense than just allowing certain version to be installed simultaneously, since the needs of users in this regard is hard to predict, in my experience.
Ion could also look in /etc/X11/ion-2 and /etc/X11/ion for configuration files first. In fact, related to that, I would prefer that ion store the default configuration files in /usr/share, and then only user-modified configuration files would be placed in /etc. -- Jeremy Maitin-Shepard
