To start with, Saladin seems to be more of an asshole now. It's weird, I used to like him over Shaxx before, but the situation has almost reversed. Every time Ghost or Shiro asks him a question, he gives a non-answer. Telling you that your idea is irrelevant, or there are more important things to worry about.
He flips out over the idea of people attacking the Temple on Felwinter peak, but why? What's actually up there? The Fallen already have SIVA, so I doubt there would be any new information for them there. Or was he just worried about the Fallen scraping the statues?
The mission with the Cannon's was super disappointing. Shiro said something about Hawks for reinforcements. But they never showed. That would have been such a great world building moment.
That whole speech Shiro gives just before fighting Sepiks makes no sense. Ghost asks a question and Shiro says, "I can take a guess." But his guess sounds dumb. He tried driving how that whole God comparison, and it just came off really odd.
The intro cinematic shows Saladin fighting off those nanomachine things with his Axe, but the few places those things show up in game don't actually do anything. The game needs to learn to not have big bads with a story of "And these big bads know how to actually kill guardians." Because we know from a gameplay standpoint that we can't die, so it 100% takes the wind out of the sails.
This makes the final chamber area really confusing. Fighting these fallen iron lords, but why am I not worried about what converted them in the first place?
Finally, what the fuck is SIVA? does it have a mind of it's own? It seems like they were hinting that SIVA has an influence over the Fallen, more than the Fallen have an influence over it. What the hell was actually going on there? Since nothing was explained, it seems like the Fallen just found a new stylist for their armor and vehicles. Like, "He you guys like these Triangles? There is just something really aesthetically pleasing about these triangles... I think I'm going to put some triangles on my face, maybe that Walker over there, too."