I took the time out of my life to read all three Metro books. Before you ask, it was mostly worth it. I'm not going to bother reviewing the books, but the tl;dr is that Metro 2033 is a good book, Metro 2034 is a good book, and Metro 2035 is not. However, what does interest me is what the latter two books can hint at for the upcoming game. So I picked out a few interesting plot elements that stood out to me as possible hints as to where the story of Metro Exodus is going.
First, I'm mostly just considering Metro 2034 and 2035 here. While Metro 2033 is a good book, Metro 2033 (the game) hits up nearly all the important stuff. Perhaps the only real thing of note that I feel like 2033 (the book) has that 2033 (the game) lacks is the fate of Artyom's mother and his phobia of rats. You see, it's never really explained what happened to Artyom's mother in the games other than the implication that, one way or another, she died. However, in the book, Artyom and his mom are both living in the metro at the start. Something supernatural manages to upset the rats, who begin to try and flee the Metro in a tidal wave of fear. The result? Everything between these rats and the exit is viciously devoured, including Artyom's mother. After this, Artyom can't be near rats without freaking out. This isn't reflected in the game, and to be totally honest I don't see Exodus trying to suddenly pick this one plot string up.
Another plot string I don't expect to see? Hunter. At the beginning of both versions of 2033 a ranger named Hunter sets Artyom off on his quest before mysteriously vanishing. Both versions imply that the Dark Ones killed him, but we're never given any confirmation in the games and by Last Light Hunter is barely mentioned. However, in Metro 2034 we learn that Hunter is still alive. He is also not the same person. The Dark Ones did get to Hunter, and they broke him in a rather unfortunate way. Hunter is now living up to his title, good for little more than killing and fighting. Seeing as he's basically not mentioned in Last Light, and in the books doesn't even make an appearance in 2035, it seems doubtful that Exodus would bring him back. Maybe he chose to live on the surface instead of going back to the Metro? It's possible, but I figure unlikely. Similar, I'm pretty sure we won't be seeing Homer, the old man obsessed with trying to put out an epic story for the Metro to give their life a little bit of meaning.
Speaking of the surface, what's going on there? Here's where we probably get to the most interesting stuff. The plot of Metro 2035 mostly revolves around Artyom's increasingly desperate attempts to prove that there's still life on the surface. Along the way, he slowly alienates his friends and ultimately discovers a shocking secret. Why is Artyom searching for life on the surface? Well by this point the Metro is hitting its limits.
I have to stop for a moment and explain something about the books and the games. It's about here the timeline gets kind of confusing. You see, while Metro 2033 (the game) is basically an adaption of Metro 2033 (the book), Metro: Last Light chose not to adapt Metro 2034 and instead went its own way. However, by this point, the games had become more popular than the books. Metro 2035 tries to make it so that both Metro 2034 and Metro: Last Light happened, despite parts of them not necessarily working together very well. So things like the Reds and Fourth Reich having a full-blown war, Miller receiving horrible crippling injuries, and Artyom and Anna getting married are suddenly part of 2035's plot despite not being in the first two books.
After the Reds and Fourth Reich managed to basically destroy each other, there's a weird power vacuum in the Metro. The trader faction of Hanza steps in, and things begin to look a little better. At least, until Artyom comes to the realization that the Hanza has basically bought out the Rangers and has turned them into their own personal task force. In turn, the Rangers have been slowly creating new problems internally for both the Reds and Fourth Reich, seeking to once again start a war. Combine this with the fact that Artyom's wife wants to leave him because of his fears that any kid born in the Metro will be terminally ill (This fear manifests as erectile dysfunction. I don't think Artyom's erectile dysfunction will show up in Metro Exodus.), a new plague spreading, and a good chunk of the Metro leaking and going underwater, and it's hard to blame Artyom for wanting out.
It turns out that Artyom is at least partially right: there is life on the surface. How much isn't revealed and is left as a mystery at the end of the book, but at the very least there is a town on the surface in walking distance from the Metro. Yet Artyom didn't count on one thing. It turns out that Miller is absolutely paranoid about the surface. Worried that Russia's enemies are still alive, he has been using the Rangers to purposefully keep the Metro isolated from the rest of the world, thus (in his mind) saving the remaining population of Russia. At several points, Miller manages to stop Artyom from getting to the surface to send a message out, had been purposefully jamming his transmissions, and even turns Artyom's few friends against him. For the book's rather downer ending, Artyom pleads his case to his home station, is soundly rejected as an insane man, and decides to exile himself from the Metro with only Anna choosing to go with him.
This isn't all Miller's doing, though. While Miller appears to be the driving force behind it, Artyom also learns that there's another group at play. Calling themselves the Invisible Watchers, these upper-class people live in a secret isolated part of the Metro where they have fine food, drinks, power, and art. It turns out that the Invisible Watchers are the remnants of the Russian government, seeking to keep themselves in control by feeding Miller's paranoia and helping push all the factions at war with each other while keeping the outside world away.
So, how much of this will show up in Metro Exodus? Well, unlike in the books where Artyom is sort of dismissed as a loony, in the games Artyom is still the hero of the Metro and has clearly gathered the support of the Rangers. Some of the trailers have hinted that Miller's paranoia will be a factor, he often mentions his fear that they're fighting invaders, but as to what extent remains to be seen. It's almost certain the Metro is still falling apart, and even in its best condition wasn't much of a home anyway, but since the Rangers are actively helping Artyom, it's likely they're not the reason for it. With most the plot of Exodus taking place on the surface, it seems doubtful that the internal politics of the Metro matter that much anyway.
In turn, this means we probably won't see the Invisible Watchers, which is a bit of a shame. If I had to take a guess, I say that Miller's paranoia will instead be made by himself. In turn, I strongly believe that Miller will betray Artyom before the game is over. How this will affect Anna is a bit of a toss-up, since in the books her stance on Artyom swings wildly depending on what he's doing (and who he's doing. Usually, it's not her. I don't expect Artyom's weird chapter-long prostitute sex scene to make it into Metro Exodus.) Ultimately, I expect she'll have to choose between the two, will choose Artyom, and the two will have to leave the Rangers. It'll manage to use the most important parts of 2035 while avoiding the stuff that couldn't make it.
However, there is one interesting little thing that I hope we see from 2035. Partway through the book, Artyom meets an overly optimistic man named Lyokha. What Lyokha lacks in actual skills he makes up for in joyfully throwing himself at every new situation and adapting to it. He's one of the very few bright spots of the book, and I hope he shows up in the game. Furthermore, during a particularly interesting time, Lyokha chooses to form a religion around Artyom, believing that he will bring everyone from the Metro to the surface, and Artyom decides to go along with it and declares Lyokha his first prophet. Ultimately it doesn't work out, as Lyokha's attempt to adapt to every situation sees him joining the Rangers and abandoning Artyom, but he's a great character that could use the spotlight.
Though honestly, as long as Metro Exodus avoided that one really weird part in Metro 2035 where Artyom compares the Metro to a concrete vagina that is refusing to give birth so its fetus dies, I think we'll be okay.