First off it's been revealed that the Chief's newest armor is just the Mark VI but with FIRMWARE upgrades. Firmware can not mean the whole armor plating was changed as well.
While I was never a big fan of the traditional Mark VI, there just needs to be an actual explanation for the change in look, not ARTISTIC LICENSE.
To me this would mean that if a Halo 2 Anniversary is made, the Chief would not be wearing his famous Mark VI look but instead the new armor.
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I would chalk it up to artistic license.