There are 2 reasons:
1. Physical appearance. MX is way too old to be AtW's new apprentice that he could get KH2 Xehanort's long hair that fast. Also, MX's voice is way to bassy to be KH2 Xehanort's voice.
2. Addressing. Xemnas, who happens to be KH2 Xehanort's Nobody, addresses the armor of Aqua as a friend, something that MX and Aqua will never ever happen (for me). Also, we all know that Xemnas had been looking for CoW (Chamber of Waking) which keeps his other "friend". I believe that this "friend" he kept mentioning is Ven. Somebody who addresses Aqua and Ven as a friend will probably be Terra.