From my research Hal is considered a sattelite development team meaning while Nintendo doesn't outright own them they do partially fund the company and have considerable influence on their actions as they own a nice chunk of their stock .
Game freak on the other hand just has agreement with Nintendo that guarantees them rights to develop pokemon games for Nintendo handheld exclusively..They are completely self sufficient...But Nintendo does owns some of their stock
I love fighting games !!! Come on challenge me !