I will say that Cortana's appearance change really stuck out to me as well (and to probably everyone for obvious reasons), but it goes beyond the MC's armor changing just because graphics capabilities are better and can do better things.

I think it served as a very obvious indicator that this is not Cortana as we know her. As you said, it's a copy or a fragment or a highly manipulated broken version of Cortana or something. Whatever the case, it's not the same Cortana that sacrificed herself at the end of Halo 4.