I'd still have to ask why Khan looks completely different since apparently nothing should have been changed prior to Nero arriving.
Soon to be answered in "Khan", the six-part mini-series by IDW Comics. Issue #1 has the change of appearance questioned. I'm supposing his face and complexion were changed after
being awakened by Section 31 in the 23rd century.
Also, to some degree, Klingons.
Line up Kor, Koloth, Kang, the TMP Klingon captain, Kruge, Maltz, Kamarag, Klaa, Colonel Worf, Chang and TNG's Worf, Gowron, Martok and you have plenty of variety
in skin tones, crests, eye-colour, etc, to allow for the unusual crest, piercings and eyes of that one
unmasked Klingon in "Into Darkness".