In the original design we did have what was called "Consequence Events" that were intended to handle relationships if you decided not to pursue them or decline a date. While there are a few spots where the game will offer another chance, we largely had to do away with these events due to the massive size of the game and how the events are organized to work. I wanted you to be able to build a friend group of the route characters if you decided not to romance them, but it turned out to be extremely complex by the time we fleshed out the routes.
Something to learn from and apply a better execution of in the Uni "sequel". Which will be entirely focused on a group of characters, but with deeper cross-pathing, and route divergences.
Nathan was a route we had to get creative with in his execution, and him coming in after all the routes had finished allowed us to plan around world states.