I just spoke to an AT&T rep and they put a note in my account to waive the upgrade fee once I sign up for another 2-year contract. So there are sill ways of getting the fee waived.
I did the same tonight as well, no muss or fuss whatsoever. I just went to live chat, told them that my contract was about to be up and that I plan to get the iPhone 6. However, I wanted to know now before I pre-ordered whether AT&T would waive this fee because, if they didn't, I would consider instead starting a new account with T-Mobile who does not charge an activation fee. I nicely told the rep that I did not feel the upgrade fee was warranted given that AT&T would be receiving a commitment from me for two years worth of fees.
I said all of this in my little introductory statement and the rep offered no opposition whatsoever she just told me that she would note on my file that the fee was waived and that I could contact them after it showed up on my bill to have them remove it. The rep was very nice - you might even say overly nice with lots of Smileys and jokes in the replies - and I was done with the whole transaction in less than five minutes.
For the record, I have been with AT&T for seven years, and this will be the third year running that I have gotten the upgrade fee waved. I have just a very basic two line plan, no corporate or FAN account
M