I've never had a problem at Denny's. They are consistently rated in the top 10 of all sit-down national chains in areas of food quality, customer service, and health and safety standards. Sure, there are some bad ones, but those are the exception rather than the rule.
In the interest of fair disclosure, I was a District Manager for Denny's corporate (1 location in Paducah, 2 in Louisville, 1 in Clarksville, IN, and 4 in Nashville) for 5 years, until those locations were franchised (most of which are now not even there). But that was more than 20 years ago, so I don't know what all has changed.
But after being in the foodservice industry for a lot of years, and food handling safety procedures being one of my specialties, I'd take Denny's any time over Flying J. There are a few select Flying J locations where their food pre, handling and sanitation procedures were well above standard, but most were coming in at barely acceptable. A few locations consistently ranked 95 or above in health inspections, but corporate-wide the average is below 80 on a regular basis. That's bad, really bad, for a national chain, and even Flying J corporate has admitted to it. There's a reason they have replaced the head of the restaurant division about every 18 months for the last 15 years. There's also a reason Flying J is finally getting out of the restaurant business and faming it out to other chains.
Denny's is good, so is iHop. Be fine with me if they'd stick a Cracker Barrel in a bunch of them, but Cracker Barrel doesn't want to do a 24 hour diner operation.