These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Harsher in Hindsight: Going back to the whole "Forerunner trilogy and Halo 4 made all of this story non-canon (well, more so than a crossover fanfiction already is)," during one of the flashbacks, Diadect comments that he can't imagine the Precursors allowing entire sentient races to get destroyed by the Flood. In comes the Forerunner trilogy, when it's revealed that not only did the Forerunners destroy the Precursors, but the Precursors were the ones who created the Flood!
Hilarious in Hindsight: Cortana introduces the Chief to an upgraded weapon that uses a drum-fed magazine. Once Halo 4 came around, we were introduced to the SAW, which is a new type of weapon that also utilizes a drum-fed magazine.
HSQ: The description of the Forerunners and their battles with the Flood. And Demogorgon is so extreme a Lightning Bruiser that even with Helm/Didact's old Class Twenty suit and its Bullet Time power, Chief still has much trouble. You know you're in this territory when an anti-matter based grenade is considered "too slow moving and too weak to be of much use". Then again, he is the most powerful demon ever.
Strawman Has a Point: Played with with Drizzt's dislike of guns. When Drizzt objects to using UNSC weapons, he calls them "Butchery," and claims that a single man could cut down dozens before he is stopped. While Chief does show him why such weapons are needed in the UNSC, Drizzt's concerns echo real-life concerns in the United States about gun control.
Tear Jerker: If you do not cry from Gazap, the Grunt commander, telling his story, you have no soul.
Lotar's rampage because of Denos' death, and the later conversation he has with the Arbiter/Acstetic/Orna.
Screw it, everything in the Epilogue was a Tear Jerker.
The Woobie: You have to feel a little sorry for Grummish as his Orcs are being slaughtered with such speed and volume that no matter what he does, it makes no difference, and he can actively feel all of his followers either abandoning him or dying en masse.