It's tricky to want to tell a story a certain kind of way and then also give players agency. More so when you're consistent on updates and it limits your ability to really adjust the dialogue as needed when you give players tons of agency.
Honestly it feels like Buu wanted to tell a kinetic story but since those tend to be less popular, chose to give us the ability to accept/reject LIs but then doesn't have the necessary time in development to make sure all types of routes are covered. So you end up with the weird mess that is the story in it's current state unless you just run full harem. That has it's own downsides since it undermines a lot of what he says to Eliza and the romance between them.
Eliza could have been the harem queen, working behind the scenes to build a vast support system based on MC's conquests but that's not happening (yet, if ever) and so it makes the MC look like some kind of glorified playboy, telling everyone what they want to hear. Meanwhile, MC is playing Pokemon, adding to his growing collection, and hopefully it pays off some way in the future content. I can understand certain characters being essential to the plot (Kira and Pearl give him story transportation that doesn't tire him out, Diana gives him legitimacy on the water since he's technically running with a pirate crew and that comes with a negative reputation).
I'm not even sure how to interpret routes where you friend everyone or choose certain characters over others since it just reads like full harem outside of not seeing specific lewd scenes.