I would love to see the build application world get some attention, in general. It has been languishing for quite some time. In addition to your request of being able to drive it from the command line, I would love to see improvements to the "IDE" side of things.
IMO, it should remember a bunch of stuff, per top level patcher, after the first time you build an application. For example it should remember whether you're building an app or a collective. It should remember any script that you open. It should be able to include things like the java framework, and skip the step of copying it in via the Finder. The build system got to a stage of "barely good enough" and never went beyond. Projects help a little, but it could go much further.