OK, so, I may have figured out why Game Freak has been a shit-show for a while. Doing a bit of a run-down of previous games, I noticed a common trend among them:
The games with relatively efficient file structure and which didn't have a complete shit-show of issues were all ones that Iwata was involved with - I.E. the games after Red and Blue, and going all the way to X and Y, which is when his health problems got bad enough that he pulled out (and sadly, died a bit later).
When we think of games, we tend think of them from a fluff and feature standpoint, rather than crunch. Iwata, however, basically was the crunch man and GodJesus Bearchrist was he important to the series, Kiwis. He pretty much single-handedly developed the algorithm that cut the file size for Pokemon Silver and Pokemon Gold, due to his experience with working with the Game Boy in the past. This is essentially what allowed Game Freak to include Kanto in those games. He also rebuilt the Pokemon Battle System for other platforms, so it could be used on other systems. Pokemon Stadium basically only exists because he did this; Game Freak didn't write anything down regarding the battle system from the original games, so he broke it down and re-did it. The later seperation of Special Attack and Special Defense also happened on his watch.
When you go and look at the games he had no hand in, such as Pokemon Sun and Moon, you'll notice, from a data and correlation perspective, that the game is laughably inefficient, with countless duplicate model and animation entries, to the point where the file size is nearly 7 times what it needs to be. That's a problem common to early-gen 3D games, not something that just came out in 2019 with a crew of career veterans.
But there's a pattern here: The most inelegant and mechanically broken Pokemon games are the ones Iwata did not work on. The implication seems to be that without Iwata's experience and "hands on" nature helping the experience along, Game Freak is back to where they were during Gen 1 and Early Gen 2, and that is very concerning.