This is a radical change but I would love it if Titanium supported using package.json as the primary config file. At first, it would have to be in addition to tiapp.xml, for backwards compatibility, but eventually it could just be THE config file. This is somewhat related to the other feature request I created: https://jira.appcelerator.org/browse/CLI-1297.
Titanium and Alloy are already VERY commonjs module based and being able to fully use npm and JSON (instead of xml) would be very nice.
I can implement this as a stand-alone wrapper to Titanium and make it (and the other feature) work but it would be awesome if it was included in the core of the Titanium CLI.