It's not just lack of agency that's the problem. The agency wouldn't matter if it wasn't for the main issues being ignored...
The "my childhood friend/girlfriend betrayed me" is a pretty serious topic and yet is brushed aside.
We get very little development in the 2 main character's relationship.
There is not enough focus on their feelings and emotions...
Honestly, if this was just estranged childhood friends instead, that would remove a major issue with this series...
The background for this story is too emotional, yet there is no emotional focus....
Like, sure, the comic romcom element should be there.... but when a serious trauma or issue is a part of the plot as well, that needs to be worked on...
If their dating arc never existed (maybe even changing it to a misunderstood rejection) that would fix 90% of this story...
Thing is, we CAN'T explore the main character and Lemon's internal thoughts too much, because nothing they do makes any sense.
MC could solve all his problems by literally just talking about his feelings to any of these 3 other characters. If he talked to his love interest about his feelings he'd have a girlfriend and there'd be no story. If he talked to Lemon about his feelings she'd know to get lost/confess she made up the story about cheating and then there'd be no story. If he talked to his friend about his ex then his friend would either respectfully distance himself from Lemon and no longer be part of this love web, or he'd lose his friendship and basically be out of the story. The only move the MC can make to keep the story going is none.
And Lemon acts like a complete idiot, else there'd be no story. She has to invite her friend along, despite it being obviously an unnecessary and fruitless risk, else there wouldn't be a story. The same for inviting MC's friend.
None of the characters have agency because if they did, it would break the story.
You're right, the fundamental problem is that the writer has written themselves into a corner with the cheating thing. If Lemon were just an ex and they broke up on bad terms with, then the story doesn't look anywhere near as bad. Could even be an interesting, 'walk a mile in their shoes' type of story. As is, the MC treats having to be his cheating ex and having to watch as his ex fucks up his love life as a slight inconvenience. None of the characters have any depth. Their relationships are stagnant. The plot is contrived.