Finished the campaign. My thoughts on the story:
1. IIRC The Weapon is Halsey's backup, as per her Reach journal she made 3 AI's based on her mind, one was given to Chief (Cortana) and the other two were put in stasis as backups, The Weapon is the 2nd which leaves a 3rd still available. Also if I remember correctly, Halsey also has a 4th which was her personal assistant called Kalmiya, it somehow lasted way longer than the typical AI lifespan of 7 years (I think it lasted about 14 years).
I think that "Cortana from Halo 5 is a evil fragment of Cortana from Halo 4" was actually written by 343 themselves and not a theory, so I think they've either retconned that or they could have still gone with it because either way our Cortana is dead and this H5/Infinite Cortana is still a fragment of her but also dead now.
Though I disagree she's a near exact copy, to me she is the complete opposite of Cortana (one of many reasons why she shouldn't take her name), OG Cortana was confident bordering on arrogance, extremely sarcastic, confident, smart, in comparison to this Cortana who is extremely naïve, not very confident, doesn't understand sarcasm, isn't as smart as OG Cortana, etc. I also see their relationship now between Chief and The Weapon as a father/daughter relationship so I hope they don't sexualise her, Lol, her design is awesome.
2. Probably all cut content, I imagine we'll have an expansion in the future of Lasky leading a small resistance with some Spartans somewhere else on the ring, I do wish some others returned but at the same time it may have been too many cooks in the kitchen, I liked how personal this story was between Chief, The Weapon and The Pilot and I think if it shoved a lot of extra characters in then it might have ruined that, we can always save them later.
Locke is definitely not dead, Hyperius actually makes mention that he kept Locke alive with the IWHBYD skull on, I would be shocked if Jun was killed too, that dude is slippery, survived Reach. I think we'll see Lasky, Palmer, Halsey together somewhere else on Zeta Halo, I doubt Alpha Nine show up at all, Locke I think is somewhere stranded on Zeta Halo but Idk about Tanaka or Vale.
Issue with Blue Team and Arbiter/Swords of Sanghelios is Blue Team were sent off on a separate mission by Lasky and Swords of Sanghelios/Arbiter would have been defending Sangheilios but when Cortana was locked down she assumingly lost control over the Guardians and that will give Arbiter the chance to recoup but Zeta Halo did a slip-space jump so there's little chance Arbiter and Blue Team know where Chief is, someone on Reddit actually figured out based on the stars that Zeta Halo's new location is outside of the Milky Way
3. Yeah, I didn't like the whole "Endless are a bigger threat than The Flood" until Angelus explained another perspective that Forerunners are most afraid of losing their power more than anything else and now it makes sense, it also makes sense that if a Flood infected one then The Flood would be unstoppable. The Forerunners are assholes though and locked them away for nothing but "they might be a threat" which is extremely shitty, Lol.
There's some theories that The Flood exist even outside of the Galaxy, at the peak of their power they could have spread to Andromeda, I also think Flood originated from outside of the Milky Way too so who knows what is lurking out there, though the simplest way for gamers is another containment breach on a Ring, Lol.
I also worry about Atriox, I hope it's not one of those "bad guy unleashes something powerful and loses control immediately" I want to see Atriox being tactical and cunning and not to immediately lose control cause that would diminish his character, I hope he has some sort of plan for making sure they don't just immediately betray him, Lol.
I think a strong motivation, aside from the fact that having something like The Endless on your side makes your army ridiculously strong, will be that Atriox wants to bring back Doisac, whether that is in their power capabilities or not, I don't know, but I don't think Atriox knows either, The Banished was created to free his Brute brothers and now his homeworld has just been obliterated, that would put Brutes on the verge of extinction, despite him not showing much emotion when it happened, I'm fairly sure something like that will eat Atriox up inside, it will also be a cool extra, almost sympathetic motivation to his cause.