Hey highwayfive,
I've work with several multi-location businesses, and for the most part, achieve location pages outranking home page for geo related search queries. Here's a couple questions I'd have for you.
**Content **- How's the content on the location pages? Is it focused on the geo, ie directions, nearby landmarks, etc.
Links - You mentioned having links in the footer going to the location pages, however do you have any main body content links that make sense to link to location pages? For example, on the the service pages, if this service is only offered at one or two locations it would be a natural fit to link to them there. Footer links are great and a good way to get a wave of internal links, but main body editorial links seem to carry much more weight.
Google+/Citations - As Zoe mentioned, Do you have Google+ location pages for each location that link back to the location page (and the location page linking to the Google+ page)? How's the citation health for each location?
Best of luck, Ryan