On the contrary, Halo2 features a pretty nice plot twist, where a faction of the Covenent joins the Humans, because they realise that they have made a huge mistake in unlocking/releasing these "Halo Rings"
It's pretty much like the WW2in a way. Picture the SS. Hardcore, well trained, Hitler loving Nazies. But, there was also the Wehrmacht, who weren't as "diehard" about killing off the Jews, Gyptsies, and everyone else. That's basically how the "Prophet Hierarchs" and the Elites are. The Prophet Hierarchs are bent on "cleansing" the galaxy, believing that they will be spared by the awesome power of the Halo Rings.
The Elites on the other hand, turn against their leaders and begin to fight along side you. Is it an amazing story? No. Is it good enough for a shoot 'em up game? Yes.
I think I understand where Hades is coming from. He likes story-driven games. Halo doesn't really provide that because it's not really meant to, it's meant to provide a few hours of blowing stuff up with rocket launchers, charging into an alien filled room and shooting in circles with a sub machine gun.