>>29426841Okay so I explained this huge theory I had involving this in a past thread, but I don't feel like typing it all out. So instead I'll post a condensed version below:
Pokemon, much like the Japanese culture they're based on, live in a prideful and massively-overpopulated world of fierce competition for food and resources. Between "fainting" pokemon and frequent tall grass encounters, there's simply too many to deal with.
When a trainer comes by to catch a Pokemon, the Pokemon either willingly gives in to being caught so that they receive care and food (easy low level Pokemon), or their pride in being trained by a truly worthy trainer who'll take them to the limit puts them in a position where they'll fight being caught as much as possible, hence why you need to lower their health until you've both tired them out, and convinced them you're a competent trainer.
Legendary Pokemon don't want to be caught, but if you beat them down enough then you've convincend them that you're a trainer worth guiding them. Unlike regular Pokemon, I believe if you were super evil for the sake of being evil, then a Legendary Pokemon would leave or turn against you.
I truly do like the idea this thread brought up that the Master ball brainwashes a Pokemon, though. It should be the one exception to a Pokemon willingly letting you lead them like I've explained above.