Wasn't there speculation before the game came out that there was some nano-tech in the suit that could let it upgrade itself? It also made sense to me that Cortana could design/implement it being bored as shit floating in space.
Just a line in Thursday War alluding to nano upgrades; although you'd think she would have repaired that damage on his chest
I personally like the new design, but I guess they didn't really explain some of the changes going from 2 to 3; although this time it was a bit more extreme I suppose. Video game reasons.