The reason the story is as it is comes from the development style, not the writers themselves. Most devs for these games use one of 3 styles:
Route By Route, where a route is done completely before doing another, has more filler but is more linear.
Chapter By Chapter, where multiple routes are done at about the same time but are more interconnected, has less filler so seems rushed but is less linear.
Sandbox, where there are no routes and content consists of events with weak flag requirements, allows more creative freedom for the devs but results in a lot of inconsistencies and recycled content.
This game is Chapter By Chapter. Nonlinear with less inconsistencies, but less filler so story is buffed by intersecting routes where possible.