To me, the only good fight in part 6 (FF) is ruined because they decide to let FF live. It would have made narrative sense for Jolyne to kill it there, and it would have gotten killed in a smart and creative way. And I say that while FF and Jolyne are the only two characters of Stone Ocean that I like.
What other fights in SO are not outright bad? Planet Vibes and Dragon's Dream, maybe? Limp Bizkit and Highway to Hell? They are the least bad fights of the part, and I'd rank them at the same level as... Krafwerk?
Anything that involves Anna Sui, Weather, Emporio and Dio's sons is terrible. Hermes is underused and should have heroically died after Limp Bizkit. Pucci is a mess and a waste of a fantastic design. The character arcs are either wrong or lame or undercooked.
Even part 1 is immensely better than that whole mess, and that's not even getting into the art. Araki was in a weird mental space during that time...