There will be the accusation, the fallout from the accusation, then the epiloque. The epilogue will change based on the choices you made, but the fallout from the accusation will be the real "meat" of the endings, if that makes sense?
So the epilogue is more modular (or at least takes the in-game decisions into consideration), while the accusation and fallout thereof is more based on the final choice you make. If so, that sounds like you're kind of combining the two possible ways to handle endings. Which honestly might be the most effective way to handle endings in a game like this (and it's not entirely dissimilar from how Dragon Age: Origins ends).
As for importing saves, I don't think I'm going to do that. Book One has been my first project and there's a lot in the code I regret having done in the way that I did. Books Two and beyond will likely have a sort of approach like that Knights of the Old Republic 2 dialogue where you answer questions about what happened in the previous games.
It's probably better that way. It helps you ignore unnecessary flags and variables, while only dealing with the most necessary ones.
You also don't necessarily need to do a KotOR2/Mass Effect 2/Witcher 3 style dialogue where you ask the player about all of their flags in a single conversation in-game early on, but you could spread those choices out over time, and have them come up contextually. Like, say, Book Two Nelson doesn't mention Tara in their internal monologue, but then they bump into someone from high school who mentions Tara and says "Hey, are you two still super-besties like you used to be?", and then you can have dialogue choices like "Yes we are", "We actually started dating", or "We actually started dating, but then we kind of grew apart", which would then set your flag for Tara Romance to "No", "Yes", or "Ended". Or Mara shows up and while Nelson is thinking to themselves about how helpful they were in solving Lisa's murder, you get a choice like "Mara was really helpful, I'm glad we're friends" or "And then we became more than friends, and that's awesome."
It could even give you a bit more granularity - like if you want to distinguish between someone who did the sex ritual with Rain because they were desperate to solve the crime, someone who did the sex ritual because Rain's really hot, and someone who avoided the sex ritual entirely because they weren't interested.
In the same way, it could even add nuance to past scenes that the current flags don't allow for. Like if the current flags are really only Romance=yes or Romance=no, you could have a conversation in Book Two that discusses hooking up with Sophia and you get choices like "To be honest, I kind of thought she was hot for a while!" or "It was kind of just an impulsive spur-of-the-moment hook up" or "It was mostly just kind of a pity hook-up because I felt a bit bad for her?"
That way you only really only have to reestablish relationships or events shortly before they become relevant again, rather than overwhelming potential new players with a ton of questions all at once (which was really an issue in Witcher 3, where they spend a full scene asking you about people and events you may know nothing about to establish all the major Witcher 2 flags). And you can define them in whatever way makes them useful for the
new game, not just to accurately reflect the previous game's world state.
I do hope there is a canon killer, though it could be fun as a DLC to have a Clue type ending that has means and motive for all 15 suspects.
In that case, we need an equivalent to the cut Wadsworth ending
where Nelson turns out to be the killer. They killed Lisa to get revenge for the break-up, and the entire investigation has actually been them acting innocent to cover their tracks, frame someone else, and hook up with a lot of new girlfriends. Or there's possibly Jekyll/Hyde multiple personas at work and the Nelson we're playing as doesn't even realize they're the killer.
Hell, maybe the real twist is that when we pick male/female at the beginning of the game, we're just picking which one is the "good" persona, and the other one we don't pick is actually the killer. They spend the whole game living inside our head, and when the time comes for the accusation if we accuse ourselves they pop out and reveal themselves.
There go my dreams of taking Tara, Soph and B while accusing everyone else to give me the biggest chance of making sure I got the right person and then celebrating with a big girly orgy.
B's definitely the killer though.