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So far, I'm most of the way through Prospero Burns, so I'm clearly missing a lot of the background material on a few Primarchs.

That said, so far, Horus and Magnus made perfect sense to me as to why they made the choices they did. Horus surrendering to his pride because he does not want to die and lost some of his trust/love for his Father after Ullanor and what secrets are being kept from him by the Emperor. I can realistically see how I could have made the same decision.

Same with Magnus. He was overconfident. He probably should have learned after the first Thousand Son fell to the flesh changer after the deal he struck with Tzeentch, but I can see myself making the same sort of desperate rationalization. The only thing that bothers me is why he didn't tell the Emperor about his vision at Nikaea. It seems like that would have been the perfect time, instead of engaging in more sorcery. I can understand the feeling of betrayal, and busying one's self with work instead of confronting disappointment is something I do, but I don't understand why he didn't say something to Dad at the first opportunity, loyal to the Imperium as he is.

Alpharius is a little more flimsy. Presented with a no-win scenario for humanity, I can kind of understand how his choice seems valid, but then again it seems like the sort of inside the box thinking we'd expect from an idiot-Primarch like Dorn.

Reading Fulgrim was painful. It felt like there were two different writers- the one writing about events with the fleet and another writing about Istvaan. It didn't feel like he fell to Chaos so much as bobbed in and out of it. Worse, the death of Ferrus didn't feel all that tragic. Fulgrim's gloating about the sudden but inevitable betrayal by the 4 secret Traitor legions didn't fit with his regrets about killing his friend. He felt too schizophrenic.

... as did Lorgar in The First Heretic. I will say it was much, MUCH easier to feel for Lorgar, but once again, it felt like Istvaan was written by someone else. Attempted suicide by Corax felt kind of hackneyed, since Lorgar had already seen humanity's horrible fate for some time.

The only Death Guard book so far largely ignored Mortarion, so there's little to go off of. The short story with Curze was fun but not deep enough.Angron and Perturabo haven't had much screen time yet.

Bad english alert!

Well Angron simply hated Emperor, for kidnaping him, Mortarion for what he percieve as usurping his right to conqer his planet. Night Hunter is pretty clear cause too.
Just reading Fulgrim so...
With Magnus and Lorgar its interesing story, I believe Magnus didnt confront Emps mainly for three reasons, first is that he knew that E is much stronger than him and if he did see something fishy with future than E had to know too but he seemengly didnt know or care from his perspective. Second is that he taked Nikea as sign of distrust against him personaly, E and others primarch clearly didnt believe him as psyker (again his perceptive), third is most likely mesh of pride and chaos manipulation.
Lorgar was imo (one of) most humane and goodharted primarchs. Loayalists was more than willing to kill traitors and traitors was willing to fight loyalist no mather price where Lorgar was not. As deeply religious he just wanted to show to his brothers "truth", he also loved his brothers (pretty much only one who did give damn about Angron) and see his brothers kill each others did hurt him deeply as he realisied its mostly be his doing. That might explain his suicidal behaviour.
Again I am fanboy of Lorgar, so take me like that

With Alpharius/Omegon I'd suggest the decision making process after the Cabal revelation was hurried for the sake of the narrative in Legion

Legion's pacing was the problem with Alpharius' motivation, for me. The entire "Oh I'm gonna betray the Emperor" scene was a Biblical two pages /sarcasm. If Abnett had decided to have Alpharius choice affected by Guilliman and Dorn's reprimanding of his legion, combined with his pride and "we are the best Legion" mentality, it would have made sense to sway him rather easily. To at least use getting his comeuppance against Dorn and Guilliman as a motivator would have been believable, but that didn't go too well. Let's all remember their reasoning for betraying the Emperor was always clouded, but it was often hinted that they wanted to test their mettle against the ultimate foe - other Space Marines.

Curze is an odd one. While he hated his own Legion for being criminals, Sevatar clearly showed Curze loved doing what he did. His actions had already brought him to the end of what he could do without being censured, and he probably knew wrecking Nostramo would have pushed him over the edge anyway.