Stock comics by genre, not by publisher
...We've found one that has actually produced some results for us: racking by genre, and not publisher. The marketing wonks at Marvel and DC probably love the idea that there are stores that consider their brands of such singular importance that, unlike just about every other retail store out there, we design our entire stores around them as an organizing principle.
But go into a 'real' bookstore sometime, and ask them for the Simon & Schuster section. In your local video store, are all the Paramount movies together?
...If we're going to try and chip away at the idea that Marvel and DC somehow have the right to use our stores as proxies in their decades-long grudge match, we need to start with making sure they're set up as our stores. I believe that begins with laying out stores by criteria that make sense to people who don't know (or care!) who publishes the characters or creators they're interested in