For me, what ruins most fast food chains, is the lack the lack of consistency from one restaurant to another. It isn't just the quality of food preparation, but also quality of service, dining room cleanliness and other factors.
Since this discussion was originally about Wendy's, I'll share an example of Wendy's. When I lived in a small town in South Carolina, my son had a job at Wendy's. I have never been a big Wendy's fan, but I went since my son worked there. They had a wall covered with awards that they had received. Some were from local restaurant reviews, but most were from corporate Wendy's. And you could taste the difference in their food. I actually go to where I enjoyed going there. The dining room was always clean. And the salad bar was always kept neat.
I've been to other Wendy's restaurants since then, and don't care if I ever go back. It doesn't even taste like the same food.
I have seen the same variation with Burger King, McDonalds and others. I saw a McDonald's in South Carolina that became so infested with rodents and bugs, that corporate McDonald's told the franchise owner that he had to tear the building down and start over. And I've seen a McDonald's that did such a good job that at lunchtime, the takeout line went all the way around the building and into the street.
In comparison, it doesn't matter which Chick-fil-a I have visited, the food is always prepared the same, the dining room is always clean, and the help is always courteous and smart enough to take my order. In-N-Out is a very close second, with only one restaurant that I have visited being on my personal do not visit list.
Variation is a killer for quality. Fast food is no exception.