Well for one thing, the CG episodes focus on an entirely different Spartan fireteam then the one we actually play as. The CG episodes focus on Majestic while we are playing as Crimson. Ultimately, this lead to a disconnection between the gameplay and the cutscenes.
As for the CG episodes themselves, there were a few annoying aspects worth pointing out: The "Spartans" don't seem professional at all. They act more like immature marines than Spartans. Palmer... eggheads.... ugh -_- Elites drop like flies in multiple episodes and don't seem like a threat at all.
The best parts were with Jul 'Mdama, IMO. He's really cool.
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I agree that having a different squad of S-IVs as the Requiem-side action focus of the narrative was a big disconnect, but I'm not exactly sure what 343 could have done about that, short of restructuring much of the series (which could have been done, yes, but I'd need more time to think about how that could work). And yeah, Palmer was a stupid bitch. As for the S-IVs, don't forget they're volunteers from other parts of the armed forces, not trained-as-kids, cybernetically- and biologically-enhanced super-serious super-humans.