Emerald did not follow the anime, nor did Ruby and Sapphire. Nor did any game, other than Yellow.Ok for koga in yellow he got a venomoth because it is suppose to follow the show and in the show he uses a venonat that evolves into a venomoth that is why its his signature pokemon. As for wattson IDK know why, but it also comes from the show because at the end he gets an electrike or it could be because he didn't have any electric pokemon from hoenn.
As for Poliwrath it fits in perfectly because it is a fighting type and It has a varity of moves. Also because the Johto region didn't have a lot of fighting types. Also no other fighting type trainer has a poliwrath so it makes it an individual for him to have to diverse him from other fighters like Bruno.
Chuck could have easily had a Hitmontop or a Heracross.