We'll definitely be addressing this. Right now a theme really only consists of a style and an image set. We definitely need to take that one step further where templates are a part of a theme as well, at least optionally. Meaning you should be able to package several, all, or no templates with a theme, that would overwrite the original templates.
Anyways, like I said. I can't really talk about this yet, as we're still focusing on getting 7.3 finalized. But as things progress a bit, you can expect some details to come.
