One of the many examples of it ruining an anime is with the gundam series. Gundam SEED Destiny seems to have sort of ruined what was established in the original series. It is not to say I know all the screw ups, but many of the alterations to the story don't make sense. I also didn't particularly like Shinn, but that was more because he was an annoying character in my opinion.Do sequels ruin an anime?
Kuroshitsuji II is probably one of the bigger examples of something that changed the story a bit too much. I'm not going into spoilers, but it seems like a lot of the choices were poor. More so how they manipulate a way for there to be a conflict and second season. I'm not saying that all sequels are like this, but many seems to do it.
Note that things like Gundam 00's second season and Code Geass R:2 aren't really sequels. They are necessary to finish the story. The same would go for comparing Higurashi No Naku Koro Ni to Higurashi No Naku Koro Ni Kai.
So, do sequels ruin a good anime or even a decent anime?
Note: The .hack franchise is similar to a story cycle or a linked story collection. That means that each part of the story can be stand alone and be understood in theory. Therefore, .hack//GU is not a sequel to .hack//IMOQ.