The franchise has to pay fees and offer specific menu items. Small restaurants can outcompete in both price and quality.
The flip side is those places don't normally get enough foot traffic to offer their stuff "near cost", so they bundle it up into serving sizes in the $$ range that can last you a couple days. And they don't have brand marketing on their side... Joe's Diner can equally be a gem in the rough or in dire need of a new cook and a safety inspection...