I know that one of the arguments I've heard for how. as it was put, "AE killed the game" actually made a little sense.
(I should mention that I have no personal argument against veteran players farming.)
The concern was that newer players would end up on farm teams while playing in Atlas Park, and then...basically end up thinking that AE farming pretty much was the majority of what the game had to offer. This would lead to them eventually leaving CoH, thinking there was very little of interest to do other than stand around in AE.
I did actually see this happen, and managed to convince at least a couple people to come back and try playing the rest of the game.
Make no mistakes, that *IS* bad for any game. Players not staying with an MMO is a huge red flag. Personally, I think at the least AE should have been removed from starting zones, or perhaps locked until a player reaches a certain level for the first time. (Similar to how Peacebringers and Warshades were locked until you got one character to 50.)
Another concern that I've heard is of course the classic story of the "AE Baby". Where you have a level 50 Fire/Kin standing in Atlas Park asking "What are enhancements?" or "Where's Kings Row?". I know a lot of players were very annoyed because they would invite a level 50, expecting that this person had a certain level of experience with the game...only to find that this player only had a good grasp of how to kill Jello's.
While the frustration is understandable, I would hope most of us helped these players to expand their horizons.
Auroxis pointed out that farming existed long before AE, and indeed it did. But AE made it so easy to suck inexperienced players in that it ended up hurting them in the long run. Not because 'farming r bad', but because...well...you'd log into Atlas Park (my home away from home, as plenty of people who played on Victory can attest.) and hear nothing but people offering AE farm runs, or people asking for AE farm runs.
Aside from that issue, no I don't think AE 'killed' the game. I think it was a monumental achievement that hadn't really been explored in an MMO before, and a brave decision to give the players a chance at the reins.