It should've gone in acs-subsite/lib/, but we didn't have /lib back then.
I put it in the acs-subsite package, because it's a template for acs-subsite ... just like a package-specific master template typically goes in the package directory, not in www. I believe there was even some discussion about it somewhere.
I agree on the desire for a standard way to store these, with the caveat that I'm thinking you should be able to install a "skin" package, which would include an acs-subsite master template, images, etc.
I don't think it's realistic for a default install to come with all the skins preinstalled.