Store personnel can't waive the upgrade fee unless its some special promotion going on. Its been a while since AT&T has done a waived upgrade fee promotion, so don't expect the store to help out much. What you can do though, is ***** to customer service once you've done the upgrade. Usually, the customer service reps over the phone can be a bit more forgiving and they have a little more power in regards to upgrade fees.
I'm also not sure why you had to fight the AT&T store to keep those features. There is no reason why they should be trying to remove your unlimited data, as it is not a requirement for it to be removed for an upgrade. You get to keep that as long as you don't remove it yourself. It should simply carry over to your new phone. Same with the messaging package. I could never live on 200 messages though... lol. AT&T store shouldn't even care about the data plan since its not really unlimited anyway. Its all the same to them. Hell, I'd use that as ammo when arguing the upgrade fee. Tell them the store was a total ***** and was trying to screw you out of your features when they shouldn't have.
In any case, the upgrade fee is mandatory (barring any special promotions). I paid it, the guy above me probably paid, and probably most of the world pays it, on every carrier. You could buy the phone at full price to avoid the upgrade fee if you really don't want to pay it... XD
Totally reasonable, especially with the kind of crap that reps need to put up with... (joking, sorta, of course).