Yeah I agree with that Andrew - it is always best to work on one site and build its strength rather than lots of microsites - however lots brands that have franchises have standalone websites from the main brand and they do well with SEO. Peter stated above that new franchises will get their own website with identical content, except contact details etc, so it is still essential to work on unique content which will help gaining links and more.
Maybe Peter would consider your sub-directory suggestion as an alternative but I think as Egol says he should be demanding about those that take on a franchise creating unique content that will fit in with the brand, benefiting everyone involved.
I don't think you can get away from the fact that creating unique, decent content is the way forward with this - after all you know what they say content is king!