As the 80's were coming to a close, you started seeing a lot of metaplot driven games (Shadowrun, TORG, etc.). It was a big "thing" going on at the time. FR was the setting that was doing that. Gary was already gone and, while Greyhawk was still around, it had been heavily marginalized. When they tried introducing metaplot into Greyhawk, it really didn't work. Most of the people who wanted metaplot had already switched to FR years before; there was no benefit to switching back to a setting that had been largely ignored for years at that point just because metaplot had been introduced to it. The Greyhawk fans weren't particularly happy either though. Many of them never wanted metaplot in the first place.
It also felt very weird to have TSR, who by that point had spent years showing nothing but disdain and scorn for all things Gygax, were now releasing a Greyhawk City boxed set. City, Wars, and After the Ashes were all slick looking products, but the writing and characterizations were atrocious. It's no surprise that AtA tanked. The FR fans largely ignored Greyhawk and the Greyhawk fans had already been colossally let down years before. Who was left to buy it?