Re: "I think Hurricane Neddy is much worse than the Fake Skinner episode"
The whole Skinner episode revolved around it turning everything upside down so badly that they all had to vow never to mention it again. I have mixed/negative feeling about it and I understand why people outright hate it but at least they seemed to know what they were doing with it, it was just something that everyone ended up wishing they didn't do. The Flanders episodes is IMHO a dumb explanation for something that didn't need to be explained and it ruined a great joke from a classic episode. Also, it had been established that Flanders has a bunch of ethnic relatives who all talk like him filtered through stereotypes of their own cultures.
I do think that Flanders became one of the characters that the show ruined, although it wasn't because of that episode. He was originally supposed to be a good guy that Homer hated irrationally. On later episodes like the biker gang episode and the Vegas episode they have him going along with Homer's goofy ideas when he never would have during the earlier seasons. Burns was probably even worse but I can barely remember particular examples of anything he does in the later seasons.