Last summer we flew to a wedding in New Jersey. We had planned to drive, but we started potty training the girls shortly before the trip. When my husband realized we would have to stop every two hours or so to find a bathroom, he decided we should fly.
We traveled Southwest because it was cheap, and we could pre-board the girls. When we got on the plane, the first thing I did was head directly to the back of the plane. The rest of the families scooped up the front seats. Why did we go to the back? I figured we'd spend a lot of time waiting for a bathroom. If you've ever potty trained children, you know half the time they actually have to use the bathroom and half the time they just want to see it.
The most important reason we went to the back is that you can no longer stand in line near the bathrooms at the front of the plane. Since 9/11, passengers cannot congregate near the cockpit. Anyone who has potty trained toddlers knows they need to go when they need to go. Rushing up to the front bathroom every time one of the girls had to go to the bathroom didn't seem like a good idea. People get a bit nervous when another passenger runs towards the cockpit -- even if it's just to get a toddler to the bathroom in time. And, remember we have twins. There would have been a lot of running to the front of the plane.
The back of the plane was great. We were the only family with small children. I'm sure the other passengers groaned when they saw toddler twins in the back of the plane, but the girls were good. Even the flight attendants commented on how nicely they behaved. We stocked up on toys/games/books/crayons to keep them busy. I was nervous about the take off and landing, but I really didn't expect their reactions when we landed in New Jersey. Both girls slept the last hour of the trip -- including through the bumpy landing. We had to wake them up to get them off the plane.