I've thought a bit about this issue. I think a distinction can be made here between:
1. The pokemon who wear almost distinctively human-like clothing e.g. Jynx, Sawk, Throh etc (and are themselves human-like); and
2. The pokemon who use accessories which aren't as "human" as human clothing, e.g. bone (cubone and marowak), leek (farfetch'd), pendulum (hypno) etc.
Type 2 seems easier to explain. These pokemon find their accessories in their habitat. For example, we know cubone isn't born with the skull it wears. Similarly, it's plausible to assume farfetch'd simply "acquires" a leek from its habitat. A real world analogue of these would be the
hermit crab, which uses shells left by other sea creatures as mobile homes; or the dolphins who occasionally wear
sponges on their snouts. Pokemon "accessories" are just a bit more sophisticated, that's all.
As for pokemon who wear distinctively human clothing, I think it's reasonable to assume that they weave these from their surroundings as well. Throh's
pokedex entries give credence to this hypothesis:
When it tightens its belt, it becomes stronger. Wild Throh use vines to weave their own belts. (Black pokedex)
When it encounters a foe bigger than itself, it wants to throw it. It changes belts as it gets stronger. (B&W2 pokedex)
But if this is true, then shouldn't the clothing and accessories differ from individual pokemon to individual pokemon (since they used whatever material they have in their habitat to make them)? Why do all farfetch'd appear to be carrying the same exact leek? Or why do all Jinx's wear the same clothing? I think there is indeed variance from pokemon to pokemon, but it's not shown in the game or anime for simplicity's sake. It's very plausible to think every cubone's bone/skull and every farfetch'd's leek is different.
One last question about this issue is how these pokemon learn to weave their clothing or use their accessory. I think the answer is instinct. Pokemon are not merely "animals", and it's plausible that their instincts are more sophisticated than shell-acquiring crabs or sponge-wearing dolphins. A fighting pokemon like throh, for example, would know how to put together material in its environment to weave its belt/clothing, while psychic types like Jynx presumably uses magic to achieve that end.
Also, since pokemon predates human beings, maybe people in the pokemon world picked up some practices from the pokemon, as opposed to the other way around. It's obvious that the alphabet was modeled around unowns and not the other way around. So maybe people learnt to were martial arts clothing from Throh/Sawk, hypnosis induction from hypno and magic robe from jynx.
It may seem farfetch'd (har har), but it's the only way I can think of to explain the prevalence of "human" practices among pokemon.