Indeed, many things are made much more difficult with the codeshare.

However, advantages to the codeshare bookings include-
(1) sometimes better pricing via AA
(2) increased EQM for status (2.0 vs 1.5 per mile in business class)
(3) sometimes more responsive handling from AA agents

I had previously decided I would never book the AA codeshare again, but am now back to doing just that because of the added EQM earnings. Besides, even with the IB flight number within an AA-issued ticket, Iberia still can't manage to do seat assignments and the like. If you are persistent and lucky, you can sometimes find an AA agent who will do seating on the codeshare flights.

To the OP, probably not much luck upgrading prior to travel - try asking at the airport.