Ok, Bob read deeper into the game than he should have, mostly because it's really just a game that used a faceless protagonist to shove the player into the action more, and a multifaceted enemy to mix up the action.
Now, what's hilarious here, is that the deeper reading that Bob railed about here, is so off base it's hard to believe that someone who's intelligent enough to go searching for the deeper meaning came up so terribly wrong. Most likely this is because from Bob's own admittance he's not a fan of Halo, so he probably hasn't payed any attention to the story line at all if he's even played the other games.
If you draw back and look at the 3 games (reach, wars, and odst don't really count because they added side stories but nothing to the main plot we didn't already know.) the idea that the "pure race" Spartans are the good guys is just plain not there at all. Sure, people assume the Humans are good because we're human and we're playing the humans so obviously we're the good guys. That view doesn't really hold up under scrutiny though. In the course of the 3 primary games the humans let loose the flood into the galaxy and spend 1/2 the time destroying the only tools proven to exterminate the flood. Letting loose the thing that pretty effectively wiped out all life in the galaxy is not exactly what you'd consider a good thing. And while we're at it lets talk about the idea that the writers are supporting the master race Spartan's sameness policy, what is the one thing that rings true for the whole of the series? It doesn't matter what Master Chief is doing, all that spartan gun slinging does nothing to prevent humanity losing every single battle against the covenant. By the end of the second game it's been made clear that Earth is the only remaining human population center. Halo 3's ending leaves an entire continent glassed, people are worried about a little co2 causing global warming, after glassing Africa all of Earth is going to be uninhabitable. So where does that leave humanity? We refused to use the Halo weapon to kill all life in the galaxy, but we also let loose the only reason to use the Halo weapon. The master race Spartans have officially helped the human race survive... not at all, and we have to look to the expanded universe novels to take comfort in the fact that Humans have a couple tiny colonies on Mars and a few moons around Sol to survive on till we can find another habitable world to drop all our refugees on.
Now then, how about the covenant. Obviously they're evil because they're against the humans. Again evidence doesn't really support this. Sure we see some members of the covenant species are evil, the EU novels reveal that the prophets knew fully that humanity was descendant from the forerunners (the covenant's gods) and labeled humans demons because it was more convenient for their religion to survive. But in the games alone we see the elites figure out they've been lied to and switch sides to help the humans hauling along a bunch of grunts who as Bob himself pointed out fight simply because those are the orders and generally in war time disobeying orders tends to get you dead slightly faster than obeying them. And here again we see the issue with the idea that the Halo games are anti diversity, as it's abundantly clear that the Covenant are not only winning, they're winning so hard that their most devoted troops have to flip sides just to stop the humans from going extinct by the end of Halo 3.
The idea that Halo is in anyway promoting the Nazi master race ideals, or is preaching the evils of diversity is the uneducated man's surface reading from the game. The same kind of simplistic insight is what leads people to think Guy Fawkes wanted more freedom in his attempt to blow up Parliament.
