The thing I have found with Pepe's, is that the newer satellite restaurants don't seem to be as good. I live in Guilford which is only about 20 minutes from New Haven so the original location is convenient for me. My family lives in Fairfield County so we've eaten at the Fairfield location and it's ok, but not as good as New Haven. Likewise with the restaurant at Mohegan Sun Casino. I don't know if it's a quality control issue, because the New Haven location still has family working there, or the ovens or what. Maybe it's because I've been going to Pepe's since before I could remember...
Modern is excellent also, and if the Pepe's line is too long I go there. On occasion I will go directly there.--some family members prefer it. Modern often has quite a line as well.
These two places are my favorite places for pizza, hands down.