Growing up in NH Sally’s was always my favorite but they are ruining their rep with these new locations that serve substandard pies at higher prices than their competitors. My experience was the same as yours in Fairfield although I haven’t been back since they first opened. Pepe’s in Fairfield has gotten a lot better over time.
My Fairfield Sally's takeout pizzas have all been good, but the dining room is a turnoff for me. I approached warily.
At its best, Sally's on Wooster St remains my favorite of the Big Three.
Fwiw, I have 4 decades of experience there that includes tragicomically epic waits both to be seated AND to get my pizza when Sally was around, and when Flo was the premier presence. I accepted the two-timer system, and it limited my visits.
When Ricky & Bobby were in charge, I again lived locally and was in a better position to pick non-busy hours.
I also enjoyed hassle-free takeouts in peak years, courtesy of friends who would call in privately (and never share the access), as well as experience friendly acquaintances who would 'jump the line' and say Hi as they entered. It's all well-told in "Pizza: A Love Story," which is the creation of people I know through music, yoga, film, and architectural history in addition to pizza. From a totally different entry point, I've gotten to know people who were interviewed as long-timers. The favored ones no longer get the perks, and have no objections to the shift. They still order Sally's most regularly, and it's still quite fine.
I'll add here that I can't figure out how to order at Modern to get it how I like it anymore. It's easier (and less expensive) for me to just get takeout from Olde World.
And still, when I've sat down and dined at Modern while hosting California friends and a high school chum from West Hartford, both of my guests loved it. The West Coast people called "best pizza ever," and I've heard the same from a Kansan at Sally's, and a Pacific Northwest couple at Pepe's.
Pepe's Fairfield has become reliably good, which really helps, because I've stayed mostly with Bridgeport & Westport friends while visiting CT to complete my move to Kentucky. I've also liked my two most recent Wooster St pies after having nearly written the brand off... though I've liked Zupp's white clam even more. And I enjoyed my West Hartford Pepe's recon visit last month.
So the Big Three are all still good, but I'm fully confident that there are at least a couple dozen CT pizza places that can fully satisfy me, and my choices vary (think "set & setting") by day of the week; time if day; where I am when the urge to eat strikes; who my company is; who has dietary restrictions; who's not a carnivore; choice of toppings; who thinks char is burnt; who needs something less dive-y if they're sitting down to eat; who wants a full bar or great beer; what takeout travels best to the beach, outdoor concert, some other great setting, or a nearby friend's house; what has been recommended to me here or elsewhere. So many factors.
Some of the claims here about what is trash or peerless seem closer to insecure macho posturing than helpful/reliable sharing of informed personal preference. My inclination is to offer the opinion that you if you follow your curiosities & taste buds, you can confidently trust your experience of eating good pizza at a blessedly high number of places. It's not a zero sum game.