Yeah, the problem with the handheld games is that they ALL tie into the main narrative somehow, and Kingdom Hearts 3 will likely play off of any game in the pipeline, so if Kingdom Hearts 3D is really the last game before the third game, it will heavily reference it.
Kingdom Hearts 3D exist because Sora and Riku need to pass the Mark of Mastery so they can defeat Xenahort once and for all. Unless they pull out some crap that they failed to explained (like they always do), this should be it.