As groundbreaking as Shenmue was, it was still quite janky in some ways and can really test a players' patience. It's quite a polarizing game that isn't for everyone. I still give Shenmue a lot of credit for its accomplishments and ambitions, but it was not perfect... but also far from being the worst.
Desert Bus cancels itself out, IMO. This is a game that deconstructs the idea of what a video game simulator should be. It was intentionally designed to be dull and was a social satire on the monotony of real world job occupations. It was Penn and Tellers way of trolling the player, which was the entire point of their cancelled Sega CD game Smoke and Mirrors.
Grim Fandango is just wrong. I have never played Okami or Psychonauts, so I cannot comment on those.
Big Rigs deserves to be there. People call this a list of commercial failures, but Big Rigs was an unfinished piece of shovelware with misleading packaging that somehow managed to sell more than it should have. Truly a game worthy of any worst of list.
Pac-Man on the 2600 was not a fault of inferior hardware, the developer who ported the game just didn't give a shit and half assed development intentionally. This was the real downfall of Atari, as it was one of the most anticipated games of 1982 that was met with universal disappointment. This game was bad and deserves to be on any worst of list.
E.T. was an ill conceived cash grab. I can't blame the developer for how it turned out, given its limited development time. It's not the worst 2600 game ever, there are far far worse on the console. But it represents what can be so wrong with the game industry.
Duke Nukem Forever and Daikatana are almost cut from the same cloth, games that were either too ambitious or lacked strong direction to make them work. I would put Aliens: Colonial Marines in this category too... but neither DNF or Daikatana tried to fool costumers with fake gameplay trailers like Colonial Marines did. Jurassic Park: Trespasser was another highly ambitious project that missed its target with a rushed development time. The game was groundbreaking in some ways and a failure in others.