Hi Alix!
That's a tough one! There are so many great dining options available at Downtown Disney! With younger boys and a tween daughter, there's a few exciting & innovative places that you just can't find back home.
For an engaging atmosphere, my top pick would be the new,
T-REX Cafe. I experienced it just last month and both the food & experience were great! There's so much going on around you while you dine as well as some 'extra' activities you can choose to enjoy following your meal. My own 'tween' daughter enjoyed purchasing & cracking open a 'geode' and discovering beautiful crystals inside it while my younger son explored the life-size dinosaur scenes. Watch out for the meteor showers! ;) Another location whose atmosphere is exciting even from outside that will surely appeal to the whole family is
Planet Hollywood.
If you have something a little 'quieter' but still family friendly in mind, some other top picks I'd recommend include Paradiso 37 which serves fantastic, casual food in a lively atmosphere or Wolfgang Puck Cafe's open kitchen and dessert bar where the kids can enjoy peeking at their meals & treats as they are created! Rounding out my personal list of Top Picks that are family friendly would be Fulton's Crab House, a 'signature' level restaurant housed in a riverboat replica at the water's edge. The view here is beautiful in the evening!
Wishing you a Magical time as you choose & plan dining for your upcoming vacation!
Kirsten