Besides the mentioned licensing-issues, Dinnerbone (the guy hired by Mojang, who used to work on Bukkit) – as well as others involved – has said that they like the opportunity to start fresh.
Things, which was done one way in Bukkit, isn't necessary the best way and given the opportunity to do it better, it's not a hard choice.
I completely understand the start fresh mentality. I just know there is a lot of man hours that went into the Bukkit API to get it to the level of features it at now. I would hate to see it take just as long to get the official API up to feature parity.
