I think they took them out, because as Worlds and movies they only made one good movie off of those stories-Like U can't fight Clayton again in Deep Jungle cause he already died once, plus that wouldn't be much of a good story, and same goes for neverland, hook was defeated in the first one and bringing him back one really fit to well-plus with all the expanded worlds this time around theres only so much space and area on a Pirate ship, plus the "Just Believe" aspect of Neverland wouldn't work anymore-it would be really weird-I know that some of the worlds that were in the first game are back in this one, but those have legit alter stories that could be pulled from the first one, cause in the Halloween Town, in the first game they never showed the aspect of Christmas town as in the movie
As for Agrabah, Jafar returns, that is a completely legit story that can hold its on in the sequel of Kh
Same goes for Atlantica, though I didn't too much care for it- They never showed the true story of Ariel and the whole situation really...
I think thats why they negleted to put Deep Jungle and Neverland in the game