>>58273174The problem isn't rarity or effort, it's that going out of your way to do most of these things are boring and tedious to the point where people would simply rather avoid them. A game turning its players away from engaging with its mechanics is objectively bad game design.
Sinnoh exemplifies this by having both one of the best and worst examples of Pokemon obtain methods. Getting Gible is fun because it's in a secret optional area that you get clued in on by NPCs talking about it and rewards you for exploring, then makes it not too difficult to come across once you reach its area. It's not some herculean task by any means, I would certainly prefer more complex ways of getting Pokemon, but it has the player engage with the world presented to them and solve based on context clues what to do in order to get something rare. Getting Munchlax, however, is torture because it's an incredibly low chance to have appear, on randomly selected trees you have no way of discerning, takes hours with each attempt due to the IRL time mechanic and takes up resources every time by having you use up Honey and having to leave to buy more if needed. This doesn't teach you anything, it doesn't test any skill, it doesn't immerse you in the world - it's just repetitive and boring.
Most Johto methods fall in the latter and even when they don't (such as Tyrogue) they just end up punishing you for even trying with the whole needing an empty slot requirement so it's more frustrating than rewarding.