Since I just noticed this series' existence, I'll throw a comment out.
First of all: In reach, the Spartans are presented a lot more individually. I'd sort of chalk this up to limitations of the graphics in previous games as well as the fact that the "only" living Spartan is John-117. In his case, which fits with his character, it's substance over style. The Spartans in general, as you kindly pointed out, are a military outfit, which makes their armor less of a point of contention, given that all militaries in the world today are issued BDUs as well as standard kits.
Once the Spartan 3s started to roll off the line, numbers swelled and the price to outfit them plummeted. Members can and do add their own personal flair to their armor/equipment when they want to. Noble team in particular was a special group overseen by ONI, thus, their available range of equipment was more varied than, say, an "off the line" Spartan 3.
Second: You were doing fine at the start, to be honest... The Covenant IS a slave army. The UNSC (Humans) are as diverse as human beings can be with varying societal facets, flaws, failures, and struggles shown throughout the course of the series. They're forced into a "quasi-fascist" (Ugh) social structure in response to an overwhelming force attempting to wipe them off the face of the universe. The racial purity context is a bit out of left field, especially considering what you said not a minute prior to bringing it up.
Third: The blue eyes? They're blue! You only find this sort of thing if you're looking for it to begin with. His head is shaved because he's in the military. If he had suddenly sprouted a head of luxurious blonde hair, then I'd say you would have more a case for the Aryan argument.
Fourth: "Pure" mono-culture vs. "dirty" multi-culture would have some logical basis had the Sangheili (Elites) not joined the Humans shortly after Halo 2. And what's more threatening? An army of grunts or elites? Or an army of enemies ranging in size and combat ability, thus making preparation for their coming that much more difficult? It's a narrative construct most likely meant to lend reason and credibility to enemy variation. Not to mention it's a chance to create alien races and, honestly, what sci-fi game/movie/comic doesn't thoroughly love the chance to do that?
On another note about the fourth point, the Covenant are technologically superior in every conceivable way. Humans, the "pure" mono-culture, are the ones who are inferior, at least in that aspect.
It really does seem like you would have had to already been looking for things like these in order to find them. On top of that, you haven't really found anything. Each instance can be readily explained or understood with a little bit more digging or, oddly enough, not attempting to divine some sort of ultimate symbolic meaning behind plot devices.
Just because others don't see it doesn't mean that it's there and you're just that much more perceptive. I like your movie reviews. They're entertaining in their own right, but have their own obvious bias, which is perfectly fine and unavoidable given the medium and context. This, however, is just trolling. :/
I'd read about this in another thread and it was being used as ammunition against the Halo series and a reason not to buy it. Now that I've seen it, I'm kind of disappointed.