I've been procrastinating reading sadly so Idk if my words hold any weight but even so... I feel like merging the routes would be best for both the story, your workload and mental health. It would also reduce the risk of the vn being on hiatus or worse so retention wouldn't dip.
That being said, are you only streamlining the story moving forward or will the whole thing be streamlined? If it's the former (and you decide to merge), decide on a point/day/event to merge the routes and make it known that something has changed in the writing. It'd be slightly jarring if the writing style changes suddenly imo. If it's the latter, maybe put out a version of the game with what's already been done as an extra download so that people can go back to it.
Also, haven't really commented since early in the first build iirc so I wanna say that I've been enjoying the story a lot. Keep at it, I wanna see this to it's conclusion! (but please also take care of yourself obv)