
I don't really see the father as a villain here like he didn't want to leave Yui but the circumstances didn't allow them to be together and the time spent separated he was working his ass off to provide a better future for his kid. I do find it unfair for the main characters but Yui living with her dad doesn't mean they'll never see each other again they can still be present in Yui's life as her uncles.
Yui's dad made a mistake asking his kid a sensitive question at a mall I think he should've done it in a private setting but I suppose he thought of Yui as a child not capable of fully understanding what it means to be seperated with others. Now I don't know if he knows Yui has separation anxiety but he definitely made a mistake here.

I don't think anybody sees the father as the villain, even the story itself is trying to portray the subtlety and difficulty that a situation like this would entail on all sides. I think the reason why people are upset at the bio dad is because there is an undertone of selfishness to his actions. He appeared out of nowhere when he could have appraised himself of the situation first and whether that was a good thing for Yui. Then he goes and tells her he wants them to live together when she's away from their official guardians and in an unfamiliar environment after just a couple of outings together. The dad wants the situation resolved to his satisfaction: him living with his daughter "like a real family", but he's never once prioritized Yui's emotional state during this process. He either didn't do enough research and expected her to behave like a baby that one can just drop and pick back up and they won't realize it (which is a very big problem if he wants to be primary caretaker), or he has convinced himself that just because he's her bio dad and reasonably cares for her, that gives him allowance to disregard her opinion (a sort of " she'll get over it in time" approach), which is also not in the best interest of the child.
Yes yes thats nice but what about the war?? Or the other guy that got summoned why add those foreshadowing plot if its a one shot
My made up continuation:
The humans of that world summoned the other boy to defeat the beast people.
The other boy got powers and united forces with humans so he could maybe save our mc that tried to save him.
Already on war both sides clashing, somehow powered boy met with our mc, they talked and powered boy stopped the war, they made an alliance, powered boy became king, everyone is happy (outside of the original monarchy and possibly church summoners who were defeated)
Also god is very powerful so he intervened in the summoning putting their hand selecting the summoned boy so would be a good one and letting mc also arrive so all this plan would be successful