I got in on the tail end of the Atari 2600 craze, and most of my collection was from trades or store clearances, but I don't remember the library being particularly bad. No one seems to name particular games when talking about these horrible 2600 games, other than ET and the bad Pacman port.
There's a widespread perception Nintendo swooped in and saved the industry with their new 3rd-party rules and policy of dissociating themselves with the words 'video game'.
I'd contend that the worst games on the Atari are roughly equal to the worst games on any system since when you look at things relatively. It's not like the concept of shovelware went away with the 2600, it just has a seal of approval on it now, which is in some ways worse because it gives a false impression of quality/endorsement.
A lot of the 'bad' games I remember from both the NES and the Atari weren't so much bad as incomprehensible without reading the manual, and sometimes even after that. The games were fun at the time, and it's only in retrospect, having played so many good games, that I realize what was bad. Even ET was fun to my 5 year old self. To this day, I still have no idea how the heck Swordquest for the 2600 was supposed to be played, and I didn't learn until about 10 years later that the Indiana Jones game was supposed to use both controllers.
I'd say either of those have a leg up on Deadly Towers for the NES, which has invisible warps that throw you into a 256-room dungeon and still seems confusing even after watching a YouTube video of a complete playthrough. Almost randomly warping you into areas of the game that make take hours and an intricate map to escape is just BAD. I could probably name 10-20 other NES games that make little apparent sense based solely on the gameplay.
Ultimately, were retailers even fooled by the fact that 'video games' were now called 'game paks'? It was obvious to my kindergarten self that Super Mario Bros was just a video game with better graphics.