you have to establish compatibility before you can worry about maintaining it ;-)
what features are you willing to give up to get your universal compatibility?
as a trivial example, if an application needs to store some data and the upstream support sqlite, mysql, postgresql, flat files, or various 'desktop storage' APIs, which one should the universal binary depend on? and why?
KDE and Gnome each have their 'standard' tool for storing contact information, should Gnome users be force to load KDE libraries and applications (or KDE users forced to use the Gnome ones) to maintain compatibility?
what if someone comes up with something new, should that be forbidden/ignored so that a universal binary can work on older systems that don't have the new software?