Bagels.
This is an unusually glib comment for me, but it's something I've missed so much since leaving the northeast that I bring back pizza and bagels with me to Seattle whenever I visit New York.
The bagels specifically, are often doughy, "sweet" (they actually add sugar in many places), and with all the wrong textures. It's odd that you mention brands, since I typically buy "supermarket/local baker brand" but I've definitely found that to vary.
Similar comment for donuts, the big brands here e.g. top pot are practically cake rolls.
(Philly also had wawa and corner cheesesteak shops providing way cheaper "decent low-end hoagies" than I can consistently find out here.)