heh, yeah. I didn't mind it either.
Well, gameplay changes would have included something like your suggestion of including an AR in Halo 2 (and the various gameplay sections already mentioned).
I was thinking no more than adding sprint (no armour abilities otherwise), and perhaps adding pure flood forms in Halo 2, but that to me is seemingly inconsequential in the grand scheme. With the missing events, I was more or less thinking about only recreating levels that fit a rampant Cortana narrative (although it's a slippery slope to a rather broken narrative given all the cut-scenes involved). A complete remake would be best (and a ton of work). Most of the "explained changes" would basically have included the visuals (art direction) and quirks related to the different engine involved, but otherwise, the level layouts/environments would be as close as possible.
A complete remake (ala Fable) is pretty much making a new game with a bunch of the design taken care of already, but there's still going to be differences due to the underlying engine and the new art that needs to be created. It'd be a lot of work to make sure everything is the same between engines. I mean, sure it was kinda neat that all the bugs & physics were the same in CEA, but that imposed some glaring technical limitations.