Hi! And thank you for coming here to chat with the crowd. That's rare nowadays -- even more so when it comes to seasoned developers like you.
I think having to go through all the girls during season 1 made sense for both intra- and extra-game reasons. Intragame, storywise, because the impact of the fatalist/dramatic ending would've been diminished if we'd done a clean/paragon run. Like... what would be the drama if the MC had only pursued one love interest? He had to have messed everything up for season 2 to make sense. And extragame, from the developer's perspective: if you had two or, worse, three endings, developing season 2 would've meant creating what would be -- if not literally two or three extra games -- at least 50% more work. Since I've been trying to develop my own stories, I know things can get pretty wild if you branch too much. It's a common technique, the "branch and bottleneck" strategy, so you don't go crazy. You could've added some variables/triggers so the girls would react differently depending on what you did in season 1, but that would be more like Easter eggs than full-on divergent paths (though it's fun anyway, and maybe you could implement that in the Unreal version).
Also, I wouldn't say the lack of choices, but the meaninglessness of them, made sense storywise from an artistic point of view. It was like a Greek tragedy; and the fact that you only realize it at the end is the trick that amplifies the impact -- it's the "Oh! Shit!" moment. In fact, it's where the real game begins. In scriptwriting theory, the loop would be the inciting incident; but the moment he wakes up and the day changes is the key event that puts the player face-to-face with his dilemma. Now he should be working toward the solution -- and changes have to mean something, otherwise the ending becomes just a Deus Ex Machina. Okay, the ending of season 2 was divisive, but I liked it. It was a turning point -- the moment of revelation when the player gets a glimpse of what's going on (continued in season 3). Now he's in the "dark night of the soul," where everything seems lost. More than ever, he'll have to take action to solve the problem. He's already trying, and you said there are genuine stakes and consequences now, but since we're still looping, it feels like he's just collecting data. For it to really end like a game -- and not just a kinetic story -- there must be consequential choices. Whether that happens at the end of this season, in an epilogue, or, if there's enough material, a fourth season, that's when you can branch without fear. You won't have to worry about tying everything back together, because the story will be over -- even if the solution is going back to day 1 and redoing the steps without hurting anyone.