So the thing is, my novel is set initially in a fairly mundane setting, so this was enough for my beta readers to assume it was just a modern day setting. However, that was sort of my intention. The MC is not supposed to know that he's living in a divergent timeline until later. But the beta readers were not happy about it. They told me the reveal was jarring and felt like I pulled it out of...nowhere. The thing is, the MC is supposed to be confused and only find out as we go about what changed world events and caused the divergence. What could be the problem here?
Listen to your beta readers, if they think you pulled it out of nowhere, then it reads like you pulled it out of nowhere. It's as simple as that, regardless of intentions. The problem is you haven't sprinkled enough hints about the divergent timeline earlier on and so you should either sprinkle in some hints or start the story closer to where the MC realizes he's not in a normal timeline.
Without reading hard so say, but the usual trick is to set up a lot of mysteries, which, after the sudden-out-of-nowhere twist, all begin to make sense. "Oh I see. Now the weird fact that his brother went from alchololic to stone cold sober and no-one mentioned it makes sense. And the way everyone kept asking the MC why he turned down a promotion that he was convinced he'd taken." As the author you can tease that it is something to do with brain injury, or a sinister gas-lighting Truman Show... But none of those explanations will sit quite right, making the actual reveal more satisfying as the reader wonders why they didn't think of it.
I did though. Maybe they weren't enough? I did go with something like that. The MC goes to a library searching for books and information that doesn't exist. But I guess no one connected the dots.
You are going to have to post something to the workshop to get a proper response. But in absence of that I'd ask whether you laid it on thick enough (answer, according to beta readers: no), and whether you gave enough clues in lots of places (there are dozens of reasons why information would not be in a library, starting with Ministry of Truth style censorship). Final question is if you make it plain from the off that it's a sci fi. You might want to keep it a secret, but like it or not people don't like to find out at the end of a book that it's a totally different genre piece than they thought.
You sort of contradict yourself here. You say the MC doesn't know at first that he's in an alternate timeline but that he's supposed to be confused. Which is it? I don't see how he can be confused unless he has some traces of the original timeline which creates doubt. A prologue/flash forward might help with readers' expectations but they are usually not recommended. I think it's better in this case to just sprinkle some events that suggest something is off from the MC's perspective but he doesn't know or have enough conviction to investigate it further, until the reveal. Even if it's just like a recurring dream he discusses with his therapist or wife where he explains that it is beyond a normal vivid dream when he wakes up, but then they convince him to ignore it.
Not from the get-go, no. But it's well established in the middle that it is. Is that such a big problem?
How far into the middle? Because if it's, like middle-middle or late middle then yeah, that's a big problem. If you market it as sci-fi, people want sci-fi straight away. If there are not big enough hints towards it being sci-fi, then chances are they'll assume it was wrongly marketed and drop the book before they get to the sci-fi parts or feel they've been waiting too long for the sci-fi parts and drop it regardless. On the other hand, if people somehow miss the marketing, read the first few pages and assume it's a slice of life, they'll get comfortable in the slice of life genre and feel pulled out when sci-fi parts start coming in. If you want it to be a sci-fi story and have it be read as a sci-fi story, I feel like you need to make it clearer it's a sci-fi story from the get-go.
If that’s your biggest hint, I would agree to add more; that’s very subtle and has plenty of mundane, perfectly innocent explanations. Maybe someone else checked out those books, maybe the library is poorly stocked, etc. Multiple, more personal hints, like the ones Mogador suggested would do a much better job of hinting that something is seriously wrong, even if we have no idea what yet. Remember the sixth sense? When it first came out, the twist was huge, no one had ever done anything like that before. And yet, when you rewatch the movie you see tons and tons of hints; it feels inevitable, like there was no other explanation. And, we open the movie with the idea that this kid sees dead people, and that they don’t know that they’re dead, and that’s what’s let us know the twist is a possible thing to look out for from the very beginning. The movie cleverly uses misdirection and audience expectations to hide the truth, but it’s always there in plain sight.
It doesn't sound like your setting is the problem at all, rather how you revealed the fact that they are in this alternative universe. So I would focus on getting feedback from beta readers how to improve the reveal and leading up to the reveal.
Your story reminds me of one I read called 1Q84, maybe you could read a bit of that and see how that author broaches the subject. In 1Q84 it's mentioned in the first chapter by a random taxi driver character that reality could be changed suddenly, but it's kind of disguised as an eccentric blurting. Also in 1Q84 there's a scene like your library scene except it's sort of the exact opposite, in your library scene he's looking for a book that now doesn't exist, where as in 1Q84 there's addition event's added to the timeline that the main character doesn't remember happening at all, a person can logically explain away missing information, but it's much harder to explain away how you could forget a major historical event, it'd be like forgetting 9/11. I would just suggest making it super obvious to the reader, very early on, that there's some divergent timeline shenanigans going on.