I know that it comes after KH2, but that's not really what I mean. KH Chain of Memories was a sequel, but it wasn't like KH or KH2, so I don't really consider 3D to be part of the direct story, like coded, bbs, com, 358/2 etc.
In KH3, I think what will happen will be the introduction of the two other organizations - the human-form heartless and human-form other things. The heartless are beings of darkness, nobodies of nothingness, and the humans aren't light, so there will be a new enemy from maybe the soul...?
Anyway, so there will be like an organization XIII for heartless and the other things, is my guess at least. I also think that they will actually enter Kingdom Hearts at the end. Also, it would be so cool if you versed sora's light-monster form, it being one of the organization. It'd also be awesome if they have mostly new worlds, much like KH2, which I loved. Especially when STITCH was introduced as a summon, cause let's face it - STITCH RULES!!!!! JK Though I do love stitch so much!