>>43865574We've seen spin-off and comments in other media combat both of these.
Gym Leaders have different teams depending on how many badges you have.
Unless provoked, most Pokemon won't attack you if they don't see you as a threat, so if you have a weak party only weak Pokemon will attack; the provoked part also leaves it open for you to still disturb legendary or event Pokemon.
(Obviously, there are examples of the opposite happening with Pokemon attacking, but it would work for sake of gameplay.)
The only outlier is trainer battles, but you could hand-wave it so easily with saying that some trainers can tell how strong you are by the look in your eyes, and if you're too weak they won't challenge you. Just have a variety of different level trainers around the world. And in addition, you could be the one requesting to challenge harder trainers to see if you can take them on if they don't approach you.
That could also work with weaker trainers ignoring you, but you can still challenge them if you really wanted (or base it on party level instead of Gym Badges, I guess.)
You could even have it work with a variety of trainer classes, a Blackbelt training some new recruits so he has Pokemon under level 15, or a preschooler with level 50s saying their older brother let them borrow the Pokemon.
There are plenty of ways to make it work; the only real factor is Game Freak's incompetence and refusal for outside help.