Modern, definitely makes a solid pie. I just do not think it is a destination stop. I believe that there is still significant distance between Pepe's and Modern, especially in terms of the crust. However, my experience with both dates back about 4 years now. Some say that Pepe's standards and quality have diminished somewhat with all the expansion of the brand that has taken place. I have found the crust to be stellar on all my visits.
I am long overdue for a New Haven Pizza Crawl. I still have yet to visit Sally's to round out a tasting of the famed New Haven triumvirate.