Ha ha, apparently no one read my post on page two. 343i stated that they were starting a whole new trilogy. Bungie handed over Halo, and 343i is simply putting its own mark on the franchise. They didn't keep the Gregorian chant theme we've all come to know, they changed up the gameplay, the sounds, etc. Basically all they've kept are character names. They want to make Halo THEIRS, as it were. Despite the divergence (which I'm still finding difficult to get used to), I believe 343i had every right to do so, and did the right thing by doing so altogether.
So, I will reiterate: the armor MC is wearing has not been altered physically, like the metal hasn't been reshaped. It is merely 343i's rendition of the MJOLNIR Mark VI. When Cortana says she upgraded the armor, she means the software, the shields, interface, etc. Maybe there was a nano-bot process for minor details, but overall, there wasn't an in-cryo refitting, Cortana didn't undress Chief, armor was not physically removed and replaced. It is simply a new design idea, just as plainly as I myself could come up with my own ideas for what MC could look like.
As far as appearances, I think MC's new armor "APPEARANCE" looks great and is rather more practical. Some of the Spartan 4 helmets I believe are somewhat ugly (and you all may contest my opinion), but this is still Halo, and I love it. It's just taken a new direction, and that's okay!