Gosh...if only you'd come to us well before you decided on just one day.
We did two one day trips, when DS was 1 and then 2, and we never found the time in the day to get over to DCA.
And then he was 3 and we had hoppers and time, and we decided "what the heck"...and found that we love DCA probably as much, if not more, than DL. And this includes our son (who is now 6). Well, it would need to have POTC moved there, but really, we adore DCA.
I'd write out a list of rides you want to ride at DL and anything else you want to do there, and REALLY see if you have time to get over there. If so, then include the stuff at DCA.
bug's land is, IMO, better for little ones than Fantasyland. Why? Because it's all out in the open, nothing is inside buildings with dark or darkish lines. And there's nothing spooky, and especially nothing with "Scary" right in the name!
Monsters Inc is a fabulous ride IMO, and we've ridden it time and time again. Toy Story Midway Mania...words cannot describe our love for it. Let's put it this way. We've rarely had less than a 40 minute wait for it, and yet...it's ALWAYS been worth it.
One quick question - does the Soaring ride make you "carsick"? My 6yo doesn't like roller coasters because he gets motion sickness easily. I think Indy will be fine since it's more jerky movement. My ds can't do 3D movies because even that motion is too real.
If it does, just have him close his eyes or look around. You can look to the sides and see everyone nearby, you can look up if you're not at the tallest row and see feet dangling, etc. Every so often I'll get a little swoopy in the tummy, and so I'll look around and it makes me feel better. Since you're barely moving at all, and most of it is just the movie, just distracting yourself or closing your eyes helps.