Darth Timefiller or not, modifying his eye color doesnt change that. He wasn't human. Yellow eyes are a part of his anatomy, not the fact that he is a Sith. Giving him human eyes doesn't look better imho, it makes him look more like a human with facepaint and horns glued on his head.

If you think he was timefiller or intended cool factor, then by all means remove the character completely, don't justify it by changing his eye color.

Personally I dont have a strong opinion about the "Sith eyes" debate, or whether or not the human Sith should or should not get the evil eye once they turn to the darkside. However I am against changing Maul's eyes to try to justify (or create) some bad storytelling. It doesn't make any sense.

In the end though, its Bob's edit, and whatever he wants he should go with. There are a ton of prequel edits and never will anyone be happy with the movie. It just ain't gonna happen. I've been thoroughly impressed with the things he has done so far.