The game was rushed and overly ambitious. I love 3H, but even I could tell plenty of corners were cut. This becomes very evident in Edelgard's route. I am guessing many of the game's faults are due to over-ambition, the jump to new hardware/HD, and probably a deadline set by Nintendo that was far too early, but FE isn't Zelda so not much leeway.
From what it seems, and granite I am basing this off just common knowledge things, the team likely had like 2, maybe 3 years of development going off the fact that Echoes released in 2017, and so did Warriors. Paper Mario also released in 2016, and Fates in 2015/2016. There was also another Paper Mario in 2020. Taking all this in, There was only a brief little over 1 1/2 year gap between releases Intelligent Systems had from Warriors to 3H. Seeing as Warriors was the basis of 3H, not much could have been done prior I would assume. To me, this seems like 3H was a title with little time and probably split teams what with Paper Mario, FE Echoes, and Warriors around it. Add in that they wanted 4 routes, and it was probably too much to handle.
Maybe the team should have stuck to one route instead of trying to 1 up Fates. Who know?