I sat with an Airtran pilot earlier this week in BC, and he had mentioned that SW was getting rid of "redundancies" up in BOS -- that is, the FL gate agents. To further validate his claim, I had noticed that same day that the normal FL gate agents I've had at BOS were "switched" to some Southwest folk looking slightly confused. Sucks, but I guess that's how it goes with these takeovers.
I asked about any upgrades as usual at the counter, and it took a lot longer than usual, but luckily didn't run into any real issues (fingers crossed for future flights).
I am (unfortunately) less surprised by the issues mentioned above, particularly since SW is letting some of the FL people go

hopefully the process will improve after SW folk are "trained in" -- but that may be wishful thinking!