Putting Greg Bear in charge of the forerunner and flood backstory. His three books is like having Dan Simmons' Hyperion Cantos dropped into the ancient Halo Universe. His work elevated the series so much from where it were after Halo 3 and Reach. People also don't appreciate nearly enough how fateful his books are to the earlier Bungie source material, whatever he added or changed were purely for the better.
The writing in Halo 4 between the Chief and Cortana. The Bungie games did not, for the most part, have good writing. I love Halo CE:s story but that's mostly because of the general pacing, mystery and atmosphere of it all, and a lot of that is due to the music and level design of that game, not due to the writing in itself.