Weak Pokemon still give you 6 turns, and that's more than enough time, especially if you find especially tanky mons.
If 6 turns and some soft resetting let you easily catch a full HP Pokémon then the RNG isn't doing its work.
And getting an end-game level Pokemon is entirely worth the soft-resetting, especially since open-world games make it as smooth and easy as possible.
Usually end-game trainers are higher level than wild Pokémon, make them at most around level 60-70 save for legendaries while making trainers up to 90+. Hack roms like Drayano's considerably increase the levels of both and it's still decently challenging.
Level 30-40 is WAY too late to be opening up the world, as that tends to be late mid-game in Pokemon. The Great Plateau takes a couple of hours to beat at most!
That would also mean reaching those levels way more quickly. And you could already easily reach those levels by the third gym even in the first gen.
Pokémon games can already be easily exploited through a bit of grinding, I avoided all non-mandatory battles in Moon with a 6 Pokémon team and still fought the Elite Four at like 5-6 levels under them.
Even then, there is no way to create a balanced challenge for the player without breaking the game in favor of low-level runs, as most open-world RPGs end up doing.
That might be true for wild Pokémon (though thematically it would make sense that wild Pokémon can't be as strong as ones who formed a bond and were guided by their trainers. And in the games wild Pokémon were already not over the 60 range), but trainers could still be divided by ranks so that you have to fight against trainers who are ranked the same as you, while higher/way lower ranked ones could be optional. As for gyms, their levels could be set as the same as the highest leveled Pokémon in your team, while the Pokémon they'd use would depend on your level (e.g. either using a level 10 Geodude or a level 30 Graveler) so that you can go in any order you prefer. All of this would make for a way more challenging game than the joke they currently are.
Also, Pokémon was never about the difficulty so much as going on an adventure, having that sense of wonder that Breath of the Wild captures so perfectly, and seeing your team become stronger. All of those would be better realized in a BotW-esque Pokémon game. Heck, you could even backtrack in places you already visited to fight trainers who were higher ranked than you before or visit places where you usually would get your ass kicked, instead of making places you already went to mostly useless once you're done with them story-wise.
It's not an easy feat, one that I doubt Game Freak would ever be able to manage even if they wanted to, but it could definitely work and be a breath of fresh air for the franchise.