The fact is in each of the recent "mergers" there was one dominate carrier and "merger" was used primarily for tax reasons. Southwest/Airtran is a straight up purchase with the money flowing from Southwest to Airtran's former owners.
However for continuity of service and historical reasons I think the sub-forum idea works best. Airtran will cease to exist but so did Northwest and so soon will US Airways.
But in the long run it makes little difference.
Keeping this information close together will allow it to be accessed more easily.
But on the other hand it's not a big deal.