Let's be honest here, I think both MovieBob and Yahtzee miss the entire point of military disapline and uniformity. You can't conduct a war if you have everyone out there running around, doing their own thing. You need to control information, and get people to the point where they do what they are told. This incidently includes being sacrificed for the greater good. Sending one group of guys into a meat grinder so your other team of guys can complete an important objective in the big picture while the enemy is busy for example (and if this example offends you, remember that wars are ugly and blow chips for a reason).
The thing to understand is that we're dealing with a military organization in these games. Even as a Halo fan I understand this, and why it's all uniform. These guys aren't a representitive of humanity as a whole, but of our military, our champions, our defenders. Us, the game players, are not supposed to need a lesson in the diversity of humanity, because we are humans. We generally don't see the civilian culture that the military is defending.
The diverse alien races being fought are uniform among themselves, each species pretty much acts the same way the spartans do with standard weapons, equipment, and an order of battle. The point being that if The Covenant was to conquer humanity it would still have it's own order of battle and so on, but would effectively be subverted to the whole like those guys were. It's also important to note that The Covenant eventually does not want humanity to join or be subverted... it wants to wipe us out entirely as a threat. I mean think about what the Titular "Halo" weapon is, and what it shows up to do.
As far as Nazi referances went, well understand that the Nazis are generally stereotyped by their military. Their military not being all that differant from any other effective fighting force. For reasons related to our current, unworkable, morality, you rarely see much about the civilian Nazi culture, groups like the Volkssturm, or the slaughters that were inflicted upon them to win World War II. Being disaplined, focused, and kept a bit ignorant is simply military, it has nothing specifically to do with the Nazis.
The bit with the blue eyes, well, understand that this DOES have something to do with the Nazis. According to some things I've read, the very first Halo books got into the backround behind the Spartan program, and how it was based on a Eugenics/Genetics program that the Nazis started in World War II to create their "ubermensch" as super soldiers. Before the arrival of the covenant there was supposed to have been a lot of fighting between human factions, and the Spartan super soldiers were created to try and resolve those wars, using technology that started with the Nazis and had apparently been being worked on sense (presumably starting with Nazi scientists who wound up with the Allies after the war via things like "Operation Paperclip"). Apparently this was contreversial enough where it was supposed to have been changed (or glossed over to avoid directly mentioning the Nazis) in later printings of the novels. In the end though the bottom line is that the guy's eyes turning blue are probably supposed to give you exactly the message it did, being a sign of the origins of the technology being used.
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One final note for anyone that has read this far (which I hope includes Moviebob):
I have read "Starship Troopers" not just seen the movie. The scenario is a lot differant than the one presented in the movies, and if you read it, the aliens they are fighting aren't quite like they are in the movies, and apparently have proxy races themselves.
It should also be noted that while the book focuses on the military mentality, why it exists, and the proper ways of fighting a war (and could be considered very anti-liberal for this reason... it's very much based on reality, rather than moral principle), the weapons being used are not anything like either the movie, or what you see in video games. These guys basically use battlesuits that can jump like The Hulk and fight with flame throwers that literally shoot streams of fire miles long. To put things into perspective a couple of these guys would render pretty much anything you've seen in "Space Marine" games, or even settings like "Warhammer 40k" irrelevent. One of these guys sweeps his flames back and forth and he's pretty much going to wipe out city blocks. The fire is so hot that it't not even going to leave flaming wreckage since when the flame passes it's so hot that it consumes everything, there is nothing left to burn.
To be entirely honest, it's been a long time, but I kind of wish people would stop making referances to "Starship Troopers" whenever some work of military science fiction comes up. The entire style is pretty unique, and nothing close to that take on warfare, the nature of the engagements, and similar thing has ever really been done.