From a character based view i can understand why Cordy wasn't exactly a major topic of conversation through season four onwards. Her main reason for hanging with the Scoobies was her relationship with Xander. I can't imagine that any of the other Scoobies would really have described themselves as being close to Cordy.
It's like in any group of friends, there are always people there that are only really linked to one other individual, say a boyfriend or girlfriend, and once that relationship ends they drift away again. It was fairly obvious in I Will Remember You that there was still no real affection between Buffy and Cordy. They weren't really friends in any way.
From a story telling point of view it was obviously neccessary to have Cordy already in L.A. by the time of City Of and so the only place to show her leaving would have been at the end of Graduation Day. Obviously this wasn't going to be possible if you wanted to end the third season with the big battle with the Mayor Snake. It would have been something of an anti-climax to then cut to a scene of the Scoobies standing at a bus station, waving Cordy off. Also there is no reason to beieve she left straight away. It could have been a month or more later when Cordy finally left.
So given the fact that there was no real place to show the "Cordy leaving" scene, added to the fact that she wasn't really that close to the other Scoobs, i think it makes most sense that we are left to our own devices to imagine the details. I've always pictured it pretty much being Cordy and Xander hugging and Buffy, Willow and Giles maybe standing in the background just to show some sort of Scooby solidarity as Cordy steps onto the bus and disappears to her new life in Los Angeles. No big, emotional scene. Just a very basic farewell to an old acquaintance.
