What if we are all mistaken and Takamine we see now is not the "true" one but is actually one from the future?
Maybe something happened to MC and she feels responsible for that so she used her power to go back and redo her high school life (which would explain how she has perfect grades despite us never seeing her studying seriously beside preparing Shirouta for university, she already finished high school and knows all the subjects), guiding him to a future where he will be fine.
My base for this theory is that her powers were not entirely explained so far in the story and the affection she has toward Shirouta that she will accept nothing short than total control in order to manipulate how will he act and go onward.
Her power - we have no idea where she got it and how it works exactly. Does it have some limitations (we can see her rewinding back anywhere from few seconds to half a day) and are there others out there who can use similar power as well?
Shirota - from her actions we can see that she is manipulative and sadistic but beneath all of that she does care and even goes to the extreme to not let him stray away. It was explained a bit by showing her past when she had some history with him but other than that nothing else.
My take - In 'original timeline' so to speak she went with him in high school but was always shy while he was always as dense as he is now. Then at some point something happens to him, we have no idea what, but whatever happens left quite a shock on her. While being consumed by grief she obtains this kind of power and decides to do entire life with him from the start, resulting in 'current timeline'. First she started working on herself, morphing from shy girl to perfect student council president so that she could assist him better. Then she sets him up so that he can also be aware of her powers and then she tries diplomacy with him. Which backfires as he wants nothing to do with her. Only then she uses blackmail to force him to go with her offer, becasue she knows that the alternative future for him is much worse than this.
I know I am giving this story too much credit but I honestly think this theory can explain the majority of the current plot.