I agree, however you could just not use it.
I found the box most useful when trying to evolve pokemon for the dex. It was so nice to not have to leave cerulean cave, go to the pc change my team, go back evolve a pokemon and then repeat over and over again. Being able to just switch pokemon in and out on the fly was so nice. Maybe in pokemon 2019 they lock the box during e4 and once you go into a gym.
I think having access to the Pokemon Box at all times is the Pokemon equivalent of fast travel. For so many the eternal argument revolves around two stances:
1) Fast travel essentially ruins the experience of the game by allowing you to not have to account for certain aspects of your journey. It has to be removed, because gamers experience the game as it is made, and having it available means it will be used.
2) Fast travel is entirely optional! If you do not wish to use it, then do not. Problem solved, everyone wins.
Obviously, not a direct correlation, but I see those two basic arguments being present here. I am sympathetic to both positions personally. I use fast travel in games that have it all the time, but, when playing BotW or Skyrim for instance, I mostly forego using it, because I am after a certain kind of experience.
For me the solution is a no brainer... just make the box something you have to unlock. I like the idea for getting it after the E4, so you have to experience your journey with a bit of challenge, but after that, there should be some event or some task (locking it behind a big monetary wall does NOT appeal to me at all), just make us earn it, and then we can have box access consistently. Given how technology in the Pokemon games has evolved (sorry) with the times, it makes sense that this could be treated like some new discovery that you now have access too.
Since they just threw it into these last games without much adieu, I have a feeling that it will just be a constant feature now, which is far from a deal breaker, but I think it does take away slightly from the original experience, ESPECIALLY if they bring back battling Pokemon to weaken them before capture. If we are just going to use Go mechanics for capturing, I do not even see why it matters.