No matter how many stories can be avoided by the player, all these side stories still have to be implemented. Too many of them, and a project that is actually quite good becomes unrealistic to ever be completed. Then, in the end, nothing remains but many stories never fully told. Especially the stories around the two side jobs are, because they are almost completely unconnected to the other stories, perfect candidates to be eliminated in favor of a faster development.
Both side jobs could be removed by the simple expedient of Sophia being given full-time hours at the school, which supposedly was what she'd applied for & been appointed to. I used to excuse her acceptance of this blatant breach of contract by any new appointee's natural & logical reluctance to cause problems on their arrival in a new job.
Time has passed, slowly for us but not so much in San Alejo. This is still time enough for staffing issues to have arisen requiring Sophia to work full-time.
As no fan of shota, to put it politely, I wonder what the eventual outcomes of the side-jobs are planned to be. Currently I'm guessing that it consists of being fucked by 2 old men, maybe at the same time, while the presence of 3 under-age virginal kids, corresponding to the number of sexualised orifices of the human body & those kids being given sex education lessons in a "hands-on" style is self-explanatory.
I don't worry unduly about these outcomes because if they ever occur, they are decades away, (perhaps not so much where shota is concerned, being 'a hot kink' according to the Dev & which moves at quantum speed compared to the tales with Sophia being her normal self, i.e. everything else) & in any case may never happen. Most of us have enough to think about within the next few days, let alone what a fictional character might do decades from now. Nevertheless, at a time when something needs to change, both side-jobs could be axed without severe disruption to the main stories. At least, IMO, this would be a good start....