1) SW is far from a ghetto airline! Right now they're the only one making a profit, without charging ridiculous fees. And you get soda and pretzels still! LOL!

2) Yes, the majors have all upped their fees. Has nothing to do with your agent or the package she booked for you. That's standard with them all. Word is out that they will reduce, or have already reduced some fees in order to remain competitive with the low-cost airlines like SW.

3)Changes to the airfare portion of your package will depend upon if they ticketed your flights or not yet. During most sales, ticketing must take place immediately (even if the balance of the land portion isn't due yet). So if there are changes to the flights after ticketing, you pay the fee. Sounds like that's what happened here.