In the past, I have always compared these two airlines first since they are the lowest cost options that are a reasonable distance from where we live. With them becoming one, odds are the fares will not be nearly as low going forward since there is no other competition that does the same type of pricing model. Many airlines generally have a base price range and then may drop fares to boost sales. Southwest and Airtran function very similar with a low price available when fares are first released but only a limited number of seats and then they have higher fares as those fill up. Since they won't have competition that works their pricing structure the same way, I would be willing to bet the pricing will start at a higher tier.
There has already been numerous cities eliminated or no longer offered as a non-stop flight following the merge. Southwest offers bags fly free...for now. Will that remain the same?? Only time will tell.