Dude, I love your very insightful movie reviews. However, I cannot help but think that you are approaching Halo from a movie critic and not a videogame critic. The primary reason that the Covenant are such a diverse race is (as many others before me have pointed out) to provide clear and interesting targets for the player to shoot at. Now while you do make valid arguments about the concept of multi-culture vs master race, those really only show up if you look at the game from the outside. Inside the game Bungie makes even the Spartans a diverse group with members from various ethnicities and Halo 2 ends with the Elites joining the humans bringing along their Hunter buddies.
Now, say for example the Covenant appeared friendly at first. Appeared to join with and aide the humans, infiltrating all strata of human society and slowly usurping control, then suddenly oppressing humans more and more until they had no other choice than violent revolution, killing these aliens and any sympathizers, also going to their homeworld and completely eradicating all of the species from the universe to make it safe for humanity. THEN I would find a much stronger argument towards it having a Nazism subtext.
However, that is not the story of Halo. In Halo, humanity gets blindsided by a hyper-advanced alien army that completely outclasses the entire human military save for the Spartans. Now while the Spartans may have some "master race" qualities about them, you must also realize that they were taken from all around the world to become these super human killing machines, and even then they got taken to the curb by the Covenant. Really, if there is anything to be disappointed about for the sake of diversity in the Halo franchise, it is that the story is really told from an American perspective. i.e. all of the majority of the soldiers you see in game appear to have American accents and even the lack of ethnic diversity among the military's brass. Then again, that can be chalked up to the fact that the game is made in the good ol' USA and it may not be easy to get voice actors in foreign languages and make them not sound like stereotypes (offset pretty well in Reach by the Spartan from, what, Bosnia?)
Also, that was kind of a low blow at the characterization in Reach. I mean, yes when you break them down the characters fall into standard tropes. At the same time, I am sure that you know how hard it is to make a character who is not some trope or another. I felt that they handled their implemented character tropes rather well and at the very least much better than other games. At the same time, my character development experience is from my Senior year of highschool English (which in all fairness my high school was a 4 year college prep course).