I am 90% sure that the boss is none other than Master Xehanort. Simple. He has an Organization cloak. The only thing I question is his weapons. We've seen him possessing a Keyblade, but the secret boss has weapons similar to Xemnas. However, as proven by Roxas and Xigbar when a human becomes a Nobody, that Nobody inherits their human's weapons. So by that logic, Xemnas should wield a Keyblade because he is the Nobody of Master Xehanort fused with Terra, BOTH of which wield Keyblades. But as we know Xemnas does NOT wield a Keyblade. If he did there would be no reason for him to attempt to use Roxas, Xion and Sora to collect hearts. So my theory is that maybe when Master Xehanort and Terra fused, somehow they created those lightsaber-esque weapons that Xemnas wields. So in short I am almost positive that the secret boss is either Master Xehanort or just plain Xehanort(aka Terra fused with MX)