I haven't eaten at a Shoneys in years. The last time I ate in one, the food was inedible, the restaurant was filthy, and service was non-existent. This was in a Shoney's located in Nashville, where their corporate offices are located. If a "hometown" location was that bad, I shudder to think what the conditions might have been in other areas. I've had no desire to visit a Shoney's since.
That said, it is my understanding that Shoney's has a new CEO, and he is making efforts to rebuild the brand. If that is so, he has his work cut out for him.
The last time I had eaten at a Shoney's was back in 2006 in Martinsburg, West Virginia thanks to winning a free dinner coupon on local WLTF "Lite 97.5" radio....unfortunately I had experience pretty much the same thing as you did. Bad food, dirty restaurant, bad customer service. Actually for a time I had refused to listen to WLTF only because of my dinner at Shoney's/ It really was that bad.
Oddly enough the Shoney's in nearby Hagerstown, MD and Winchester, VA ( recently closed ) weren't that bad the few times I had ate there over the years..but that one in Martinsbug.
Winchester, VA...what really hurt the Shoney's restaurant there was the Shoney's Inn motel next door. Even though the two weren't related a lot of folks assumed they were ( for starters the logo was the about the same ). What was once a fine motel in the 80's and 90's ( actors Paul Newman and Tom Cruise had stayed there in the 80's when a they attended functions at Summit Point Race Track in nearby West Virginia ), well by 2000s the place wasn't fit for rodents much less people. Bed bugs, dead rats in the indoor pool, broken vending machines, owners who didn't care, come to think of it I believe there was even a murder or two in that motel. Anyway way too many locals assumed that since the Shoney's Inn was bad then Shoney's the restaurant next door had to be just as bad as well so many stayed away.
The Shoney's Inn in Winchester is now America's Best Value Inn or something like that. Not sure what the conditions of that place is now.