September is the quiet time of the year, that's why it wasn't crowded.
For the summer time, I'd go between 05:30pm and 06:00pm. Rush hour at all the restaurants is 8pm, and the wait will be 1 hour. Everyone thinks the same. Most visit the parks, get hungry at 6pm, and by the time they head over to the restaurant from their hotel, it's 8pm. You have to start thinking about your dinner plans earlier if you want to beat the crowd.
Same thing for lunch, everyone goes at noon after thier stomach growls. Don't wait for this, go at 11:30am and the lines will be shorter.
The good thing about the Citywalk area, is you can get a drink to go from a bar in a plastic cup, and walk around with it. Or you ask for a menu and decide what you want while waiting. Then when your server shows up, you order everything. The menu for Bubba Gump and most restaurants is posted in a glass display case outside.