It seems clear to me that you suffered damages because of Airtran, but airline delays happen all the time, and it's a risk you run when you book a tight connection, so I expect you might get more satisfaction out of arguing with the next door neighbor's cat. That being said, it never hurts to ask, and I've been surprised before by what AirTran is willing to do to keep people happy, especially Elites. At worst you could probably wrangle some more vouchers out of them.

Have you considered taking it up with the ground transport people? Seems reasonable that if your transport needs were still taken care of by the same people, then they might be inclined to waive the cancellation fees.

As to "having a case" I'm no lawyer, but it seems like you don't have any real cause of action here. FL got you to your destination in one piece and obeyed the law in doing so. I'd be mad as hell too, but what would you argue... it doesn't seem negligent, and while sloth is a deadly sin, i don't think arguing laziness would hold up in court. If it would make you feel better, mentioning it to CS would probably wind up on the FAs record, disciplinary or otherwise.