It actually seems to be a running theme that they can put out very good designs for artificial objects, from armour to weapons, to vehicles. This is in stark contrast to their plain human designs in particular, which are rather... cartoony or plain ugly. Even the last cut-scene of Halo 3, you can see blocky heads for the troopers. Could they not have spent some time to make it look decent for the one scene?
The brute chieftain, I thought, was a very solid creation, but once you start taking the armour away.. it just doesn't look good. Maybe that was the intent - bad ass armour to cover plain-looking creatures - but there is the choice of making the creature bulkier and more menacing, which was not apparent. Up-close, I actually liked the Grunt design, and when you actually look at them, you can see the menacing eyes and the spiny details on their pop-eye arms. But there is indeed a disconnect when you start paying attention to the humourous undertones. As you mentioned, it's been like that since Halo: CE, and it's been a signature of sorts that unfortunately clashes with the mature advertising for the game.
Again, intricate details for the elite armour and Prophet of Truth's crown and all, but they seem to fall flat as far as facial designs go. While I can understand lower detail assets in-game, I think they should have gone the extra distance for the cut-scenes, which they did from a lighting and shadowing point of view, but that was it (not to belittle those qualities) and it seemed a waste with the models being less than stellar.
Maybe the only thing they got right with characters (from what I recall) was the detail in the eyeballs.