I used to believe that Zexion was the Enigmatic Man before, too. But after playing Reverse/Rebirth, I no longer think that. While it's true neither uses physical weapons and both have a somewhat "removed" personality (Err, for lack of being able to explain it better.), I don't see the Enigmatic Man having to use sneaky tactics to beat someone like Zexion did. Zexion's D Report profile also says that he doesn't like to get his hands dirty, that seems to be the opposite of EM since he didn't appear to have any problem fighting against Sora.
There's also the fact that Riku Replica "killed" Zexion, apparently without any trouble. If Sora and Riku could beat Riku Replica senseless, it's very likely that Zexion is nowhere near the level of EM. ... Then there's that whole appearance changing ability Zexion used. That's really the only power we've seen Zexion use, and it also happens to be one the EM didn't use. (Not that he'd have much reason to use it during a battle, though.)