Stopped by Flatbread Company in Bedford, MA this past week (small chain, mostly in northern New England). We had their Jay's Heart - basically a tomato sauce & cheese pizza. Simply outstanding, possibly the best pizza we've ever had. I was leery about the flat bread in their name, but their crust was more of a thin, but not crisp yeast bread. The tomato sauce evidently made on site using canned, whole tomatoes had much flavor with the cheese topping having a nice bite. Baking in a wood fired oven provided the crust with a nice flavor. For those wanting natural ingredients, the flour is reportedly non brominated / non enriched / organic, their sausage is nitrate free and their other ingredients seemed to be quite natural, but none of that scared us away. A bit pricey, but well worth the quality.
IMO, Pepe's has some significant competition. http://www.flatbreadcompany.com/