I don't think people just wished they had a certain power and they magically gained that ability or the fruit magically sprouted out of the ground. Pople's desires served as an idea for someone from the past to artificially manufacture fruits that give someone such power upon consuming. Vegapunk himself managed to do this by studying ancient science.
All supernatural powers in OP can be explained in one of 5 ways:
1. Haki
2. Science
3. Devil fruit (probably just very advanced science)
4. Race (lunarian flames, Sulong, etc.)
5. Bloodline (voat)
Roger
Rayleigh
Shanks
Mihawk
Garp
None of this characters have shown anything out of the ordinary, just high haki proficiency and combat skill.
Sanji is a genetically modified human with partially artificial body. He is kinda similar to a homunculus from FMA. So his powers can be put in the science category.
Zoro's Ashura is a bit of a headscratcher, but it could be explained two ways:
1. Bloodline: the question of Zoro's lineage is still out in the open, we still didn't get any answers to who his parents were and why he resembles Ryuma or Ushimaru. It could be some kind of Shimotsuki family specific power.
2. Haki: It could be just an ethereal manifestation of Zoro's willpower. After all it's not like he actually grows extra arms and heads. It's an illusion. It's something his opponents see when he releases coc (kinda like a hallucination), since coc basically is something like an intimidation brought to extreme levels.
