I don't see giving the player more freedom as a problem, to be honest. Maybe it's more a matter of habit than a real problem, since each girl has her own character arcs (where the progress of the story really is): For example, Maxy during the first minutes of the game is not the same as at the end of the version.
In version 0.7 the "Best Match" were added where they connect the stories, but nothing is mandatory. I like to think that the story unfolds with the player's actions and not just leave you as a mere spectator of a linear story. Lucky is your alter in the story and what happens is an average of Lucky and the player, as a synthesis represented in the game's story.
Yes, it could be a linear story, but it would lose the essence of being a video game, where the interaction is part of the narrative and here that interaction is important for the meaning of the end of the story.