Very true. South park and Family Guy to name a couple.Yeah, they were all from different seasons, but from the same era (seasons 9-12).
Season nine was when Mike Scully took over as showrunner and more of the older writers started leaving. A lot of people blame Scully for making the show decline, but it was going to happen regardless. It's not normal for a show to be GOAT-level after nine years, and there were more cartoons coming out that were inspired by The Simpsons and had new, fresh ideas.
I think prime Simpsons might be the greatest run any television series has ever had. You're talking about a minimum of eight seasons of classic episodes. Most shows don't even get past three or four years before they start falling off and The Simpsons was able to stay consistent for almost a decade.
Also, my theory is that the real world was starting to become more absurd than the show, especially with the internet, the Bush era, etc. These other shows were going for more raunchy jokes and the Simpsons kinda had to stay in the box they created for themselves. No sex jokes and the only real violent episodes were the Halloween specials.
Also, at some point they focused more on the jokes than storylines for episodes. In other words, it's almost like they started to write jokes and then created a weak storyline around it rather than the opposite.