Broken Base: Jupiter. Some people see it as a solid, no-frills comeback that does a good job at mixing in elements from all three of their studio albums, while others see it as a pile of horribly produced garbage that relies solely on the name attached to it to get by. And then there are people who think it's a solid album despite being horribly produced. (It helps to find one of the fan remasters floating around the Internets. ...Or So I Heard.)
Fandom Rivalry: While very few people dislike either band, Atheist vs Cynic wars are not unknown. They're pretty tame compared to most fights over metal, but they can get fairly heated at times.
Tear Jerker: Kelly's account of the night of Roger's death; it can be read in the remastered Unquestionable Presence album booklet.
They Changed It, Now It Sucks!: Some people's reaction to Jupiter. Although most of the complaints about it seem to be based in the horrible production - see Loudness War on the main page.
Vindicated by History: They barely toured during their original run, had constant label issues, could not hold down a lineup, and never really recovered from losing Roger Patterson, and Elements was a swansong release that was basically them doing whatever the fuck they wanted to do because they were breaking up and it didn't matter if people liked it or not. With that in mind, they still managed to influence a vast amount of acts, and the rise of the internet helped get the word out about them on a broader scale and introduced them to younger listeners, and generally helped provide them the success and eventual stability that eluded them at every turn back during their original era.
, Enthralled in Essence