Haven't read any of the the novel myself, so this is all based on what I've read in the manga. I think part of what helps on this front is the fact that I'm a more recent reader of the manga, so it's easier to retain and follow along with everything since I haven't been affected by the windows between releases (which might be part of what's hurting the series for you, not sure, I know it affects some.)
It is true that the series hasn't really done much to touch on what is and isn't important to be followed exactly, though that's pretty true of most series with a similar premise that we won't really know about what constitutes a major deviation until the characters note this fact, so the fact I have experience with something similar might be helping me on this front. So far we know that the main party for the game's main character is fairly important, the results of the school festival won't change much and from there it kind of comes down to perspective, like how I imagine associating with Tenma is more of a non-issue because that just affects the romance side of things, and not the main plot (pretty typical for these types of games if you've ever played something like Trails or Persona.) Similarly, Satsuki's situation should be fine since she generally keeps her strength hidden, like Butao does, and so long as she remains on the sidelines since, iirc, she just kind of disappears from the game from that point, so what is one more background character really is the logic (especially since it was considered a necessary change, much like Butao helping his family to get strong so they don't die in what is coming.)
Honestly, it's fair that you find his logic and reasoning to be inconsistent, and you don't even have to fully agree with my analysis, everybody has their own way of thinking about things and viewing the world. The big thing to remember with our MC is just that he too is human. He wants to only view things objectively and in a way that only reflects his self-interest, but, in the end, just like most people, he finds himself betraying his intended logic in favor of his emotions and his self-interest in favor of his empathetic side, which is all very common for someone we have learned tended to spend is life isolated from others, no family, no friends, just him and his games against the world, but, bit by bit, he's being forced to recognize that he is no longer alone, reflecting on the days that he once thought weren't "lonely." (Sorry for this last bit of rambling, I like to psychoanalyze characters like this and pick apart what drives them to do x, y and z cause I find the human mind to be rather fascinating.)
That all being said, do I think this is some phenomenal story that has no flaws? No, definitely not, the criticisms aren't unwarranted and there are aspects of the story that could be better, like I do agree it'd be good to have a bit more clarity on the MCs goals overall, and some of the pacing can be rather awkward. I do think that people are too harsh on it though, and some criticisms just flat out don't make sense (like the early criticism that "no gamer wouldn't spend ages customizing their character," despite the fact that plenty do when they just want to jump straight into a game they're excited about,) but it's all a matter of perspective, and so the best advice I can give in circumstances like this is to turn your perspective around and see if maybe there's some angle that you might have just missed, and if you don't see it, that's okay too, it's something that can take practice and sometimes it's just a sign some things about the story just don't click with you (there are plenty of stories I can't ever resonate with, no matter how hard I try, like how I just don't get why people love The Emince in Shadow so much, even if I look at it from the lens of satire or parody.)
