I've got to totally agree with the OP. AE has most definitely CHANGED the game very significantly - and, in my opinion, not in a way that I like. I've been playing off-and-on since Issue 2, and I'm not sure how much more I'll be playing. Its markedly clear to me that non-AE teaming is a fraction of what I've experienced in the past. Although TF/SF and Trial teams can be found, I haven't been on a PuG doing story arc missions at all since AE came out - not a single one. Also, when I have been on teams, the overall quality of players was noticeably lesser. (I'm fine with the learning curve that players have though, so that's not really a complaint, more of an observation.)
I have several toons on several servers. Most of the SG's I've been part of have very few regulars any more. Many of them just don't play as much any more. Or, at least, they're not playing their toons that are in my SG's or the ones that I used to team with regularly. Hehe, maybe they "drank the Kool-Aid" and have been PL'ing new toons in AE.
COH is still on my radar though. I still play (less often), and still hope that some of the next issues will provide some content and features that will make it better for players like me. For those that really like AE, that's great! Like I said though, AE has really CHANGED CoH a lot - a whole lot!
