I thought that by the end of "Chosen" the true core of the Scoobie's was Buffy, Willow, Xander, Giles and Dawn, and I thought they were fine with each other. Sure, pretty much since S4 there had been some rocky roads traveled, but they came together at the end.
And you have to remember, they are different show, with different characters. I liked how the interactions between Angel, Spike, Wes, Gunn, Fred and Lorne were unique from what we saw on Buffy. And while the Scoobies seemed to grow apart a bit, and then back together, I thought that Team Angel really splintered (and on a few occasions, broke) more than once over the course of the series. Despite that, seeing them come together slowly through S5, and then in such an awesome and fantastic way at the end, was really special. They had been through so much together, often BECAUSE of each other, just as much as Buffy's team, and the way they reunited was very cool. Illyria was a huge, huge part of that. I thought that she (and Fred's death of course) brought them back together quite a bit. And the way she develops and grows closer with Wes was a tremendous story.
I actually think that after all that had happened with Team Angel, his famous line at the beginning of S4 in "Deep Down", the "we live in this world as it should be, to show people what it can be", and about how what's come before doesn't matter, it's the NOW that matters, was very fitting with "Not Fade Away" and how it all ended with them fighting the good fight, together, because that's what truly matters.