When AA issues upgrades on CX (soon to be discountinued), I'm told there's a reasonably complicated procedure involving ticket reissuance, a miscellaneous charges order, etc. Combining the fare the pax paid with the AAdvantage contribution (in support of the upgrade) does seem more complicated to me than a straight-up award ticket in a premium cabin (for which payment comes only from, say, AAdvantage; save for taxes).

Again, I don't want to say that this is the way it should be -- I think the paperwork is abominable, and I too would love to see more upgrade opportunities. But, being realistic, I'm just not hopeful.