It's a moot point now with the full dismantling of AirTran in the next couple of years, but I agree that the lack of a consistent elite upgrade procedure is maddening. You find some gate agents who are very proactive, and upgrade elites in order of check-in time; others who upgrade in the order of who approaches the podium; and others still who don't care at all and don't do upgrades unless asked.
A solution would be better IT--have an automated upgrade process like Delta. But of course Southwest isn't going to invest in such a thing with business class going away soon.