That particular idea was solely if we give pokemon a higher intelligence. Assuming numerous pokemon have a higher degree of intelligence, it would make sense that you dont necessarily have to capture them with a pokeball in order to be their trainer. If they so choose they can submit and allow that type of relationship to happen. It would be a good way for Rebels to aquire their pokemon since pokeballs would be hard to come by for them, and would add another aspect to their stories. Youre not just in hiding and on the run alone, its WITH your pokemon, outside of its pokeball and everything.