I've thought about this before,here's my theory:
When you attempt to catch a pokemon, the pokeball not only stores the pokemon inside of it, but tries to alter its genetics as it does the 3 "wiggles." For example, cats and dogs have genetically evolved to become domesticated, becoming friendly to humans and obeying orders. A pokeball can do this much faster than natural (real world) evolution can, and makes pokemon domesticated. Some pokemon, like caterpie, poochyena, hoothoot, etc. have a high catch rate because their "domestication genes"are easier to change, meaning they're less threatening and powerful pokemon who are already pretty docile. Then you have pokemon like tyranitar (pseudo-legendaries) and, even more so, arceus (legendary) whose genes are much more hardened to be powerful/threatening; they are basically the furthest thing from domesticated. Thus, they have very low catch rates and usually only higher quality/more technologically complex pokeballs can capture them. A capture will be successful when a pokemon's genes have undergone enough re-sequencing to make it submit to being captured, thus making it a trainer's pokemon.
