A good comedy doesn't need continuity. But once continuity is established taking it away does not make any sense. You either consider it important or you don't. You don't just decide one day after adhering to it for years to remove it. Or at least if you do such a thing you can expect some people to be put off by it. It's like how South Park would have Kenny die in every episode with no explanation given as to how he was alive in the next episode. It was funny so it didn't matter. BUT it was also established from the very first episode that this was how it worked. It isn't like one episode, several seasons in, Kenny died and then was back in the next episode with no explanation given. If a non-Halloween episode of The Simpsons ended with Bart getting decapitated and then he was alive in well in the next episode with no explanation given it would probably kill off the show's viewership.
What I found so bizarre about the Principal Skinner thing is that who thought that was a good idea? I think any intelligent person would figure that revealing that a regular character was in fact an imposter would turn off SOME viewers. Is it really such a hilarious idea to take that kind of risk on? Is it going to benefit the show in the long run or create all sorts of new episode ideas? I mean shows change all the time. We'll see new kids being born, characters getting married, characters switching to a new job. There is a risk of turning off viewers with such a change but such a change can also allow for new storylines and ideas. But with this Skinner thing it was a one-time episode. You're going to completely change a character, with a really ridiculous storyline, for the pay off of ONE episode? It's a huge risk with minimal reward.
Hell, retcons are rarely a good idea. In real life people grow and change so if a character changes over time it is a least realistic. Even if the character turns into someone the audience doesn't like they can keep the fond memories of the past. When you change the past you piss all over those memories. It's the difference between your wife leaving you or finding out your wife NEVER loved you and the whole thing was just a big trick. How do you feel when you find out someone has been lying to you? That's what a retcon basically is.
So adding to the whole "who thought this Skinner thing was a good idea?" thing you're basically revealing to your audience that you have been LYING to them for 9 years. Why would you think this would go over well? On one hand the audience feels the same way the characters did except that the characters decide to just act as if the fake Skinner was the real one all along at the end. The real audience can't do that. You can write the characters to forget about the whole thing but you can't make the audience forget. So we all feel like the characters do except the resolution for the characters does not apply to us.