AK: Flame Tree BBQ (nice, quiet seating by the water and the menu has a nice variety)
MK: Columbia Harbor House (check for seating upstairs which has a nice view, and CHH also has a lot more than the typical pizza, burgers and fries at CS spots)
DHS: We don't eat CS here. At lunch, the Sci Fi really isn't that much more expensive than CS, and for a few more bucks you get to dine in a really neat atmosphere. We love the milkshakes!)
EP: Sunshine Seasons (amazing variety, great desserts and something for almost everyone)
At DTD, Wolfgang Puck Express is like a TS/CS combination, but at CS prices. A fantastic menu and really high quality food. Try the creme brule!
At Coronado Springs, their Pepper Market is also a fantastic option. They have sooo much variety and everyone I know loves it.
If you're staying at a Disney resort, their food courts are usually pretty decent too.
Have fun on your trip!