This merger is finally moving along at a good pace. Just a couple of weeks ago systemwide upgrade reciprocity was announced between United and Continental. As of a couple of days ago, the same is true for confirmed regional upgrades.
The process is a bit cumbersome. You have to call the elite line (be it Continental or United) and then literally transfer the confirmed regional upgrade to your frequent flyer account with the other airline. This requires your accounts to be linked. So it’s not the simplest process in the world, but it’s now possible, should you want an upgrade advantage on one of those impossible transcons.