I'm telling you guys, the main reason KH2 was delayed for so long is because Nomura edited out a few things from the original version and added several new things. For example, in the original version( there's some screen shots of this), the castle in Hollow Bastion was exactly same as it was in KH1 but in the new version the castle is pretty much in ruins and the FF characters are rebuilding the world. Also in this new version, I do believe that the whole scene on Hollow Bastion where Sora pulls out his keyblade and charges the unknown while wacking away the heartless has also been cut out and replaced with a new scene. Plus in the original version, I do believe Sephiroth was not in the storyline. But I think because of popular demand, Sephiroth has been infused into this new version as well as Tifa.
So as you can see, the delay for KH2 is mainly because Nomura kept coming up with new ideas to improve the game. And there are few other edits that I won't describe right now.
However, there is also a possibility that Nomura and Square intended to make two different versions of this game( meaning the Japanese get a version and the U.S. gets a different version). Reason I say this is because I heard that in the Japanese version of KH2, Captain Hook is not in the game. But in an article long time ago about the English version of KH2, it was confirmed that Haley Joel Osmont was going to play Sora, the guy who played Hades will reprise his role, and the guy who played Hook will reprise his role as well. So for some strange reason, there is a chance that Square intended to have two different versions of KH2 and we are the ones who are going to get the original version( meaning that Sephiroth may not be in the game at all but Captain Hook will be).