IMHO, the change fee makes perfect sense and helps fuel this transaction. The practice is called, "up-selling".

When a customer has purchased (or made the decision to purchase) something, the company then offers something that they anticipate will have higher value to the customer for more revenue. The most common example of this would be a fast-food vendor suggesting to a hamburger purchasing patron, "Would you like fries with that?"

In this case, AA provides a more valuable item to the customer, a direct flight, for more revenue. Also, we might assume that AA expects that this has reduced thier costs and has probably, at the time that the OP was called, valued the opportunity cost of providing the direct flight at less the opportunity cost of freeing the other segements for other patrons.

Seems like a "win-win" to me.

Of course, they should anticipate that an elite AAdvantage member will be concerned about the comfort of their frequent travel using thier upgrades, and should have the systems in place to prevent damage to the to the preceived value through loss of upgrade priority. While AA could further sweeten the pot by offering to process the upgrade immediately (for an additional fee?) this might have downstream consequences on the perception of fairness by other AAdvantage members.