The Whispering Canyon is wonderful and the food has always been good when I've been there. I took my nephews (8 and 6 at the time) but haven't taken my kids yet though because I feel they are a bit immature to really get into it yet. My son just doesn't follow a crowd yet and the kids in that restaurant huddle in a circle and play games and ride stick horses around the entire restaurant. You can definitely see your wee little one the whole time, but your DS or DD may not feel up to playing/hanging w/ the other kids. Mine would be twirling in an opposite corner all by himself. Go figure. So I'm waiting on that restaurant. But the food and service is very good and your 2 yr old may be happy to watch all of the action. So I would still go since it is in your resort. Wonderful place.
I've been to 1900 for BF and it was wonderful. The characters were so friendly and spent lots of time w/ us.
If you like fish, the Coral Reef is a good restaurant and has glass up to the ceiling w/ an aquarium on the other side. Your 2 yr old might enjoy watching the fish swim by while you are munching on your entrees.
I'm going to the Biergarten in Germany this trip w/ my 2 (almost 3) yr old. I haven't been there in years but I hear it is lively and fun and might entertain a 2 yr old.
The Rainforest Cafe might be fun (at DD they have a playground nearby to release some energy) if your child can handle a little thunder and rain. Mine can and I will probably go there this trip as well.
Almost every restaurant at WDW is kid friendly. We took my son when he was 8 mos. old to the YS, CG, AP and lots of other "fancy" restaurants, and he was well behaved and welcome everywhere. They just may not be entertained as well in some. A lot of posters LOVE Artist Point in the WL and you could go there as well. Fancy, but still kid friendly, just no entertainment. The food is from the Northwest like Salmon and Venison which are not my favorites so I don't care for it as much as most.
Lastly, you may want to look into the Hoop de Doo Revue. It is a marvelous, although Hokey, show and most small children LOVE it. They get to stay seated (so no pressures on Mommy to let them out of their seat), but they are given washboards and pots and such in order to make lots of noise (er, I mean music) during the show. I have always found the food to be good, although maybe boring to some.... baked beans, corn on the cob, fried chicken. You must make ressies though and I think you pay up front.
Hope this helps a bit. There are SO many good ones and it is hard to chose. I have to miss several of my all-time favorites every time I go. So most likely, whatever you end up choosing, will probably be just fine. Enjoy your trip.