In a game where it appears that the objective is identity between the characters, they have failed to do that. Examples:
Noob-Smoke is a perfect example. Could have been 2 great stand-alone characters with awesome stories, but no. they have to be the sub-boss (which basically means no story of their own) AND 1 character.
Li Mei: Goes from underdog fighting to save her people to just another bodyguard of the bad guy. See also Kitana and Raiden (possibly)
Mileena/Baraka: Sure there's the gender difference, but they have practically the same face, the same alignment, as well as the same motive (or so we think). IMO it would have been better if one was the anti-other.
Ermac/Kenshi: Aside from the weapons and stances, you have two characters with practically the same specials and I think it's safe to assume that they will have very similar fatalities as well. Also, the teacher-student thing has been done (bo' rai cho-kung lao/liu kang)
Kira: Wow. Easily could have been a cool character with the whole female Black Dragon premise. But then they had to give her the specials of Kano AND Sonya. Now, I don't know your opinions, but that's laziness if I've ever seen it.
Kobra: Looks too similar to Johnny Cage in the screens I've seen for my taste.
Hotaru: Another character fighting for his own purpose who has mistakenly aligned with the baddie. See also Scorpion.
Dairou/Darrius (forget which, but I think Dairou): One of them looks like a psuedo-Kung Lao without the hat. On a side note, Darrius is the next in the "add black guy so we don't get called racist" scheme.
Sub-Zero: If Frost is in Deception, then he must be added here. Come on, a female that looks almost exactly like Sub-Zero and has moves that were discarded in DA? Please, Boon. Get off your lazy ass and put some originality into this series.
Now, this is not to say that these characters are not awesome (because ermac, hotaru, and smoke especially look pretty bitchin) but IMO there are just way too many similarities between certain characters.