i didn't take them out gyms are there but there not gyms since the tournament is going on each gym is occupied for round like the water gym has qualifying rounds for water and blah blah blah so gyms cant acctually be fought until the end of the game and for pokrmarts they are there and pokecenters too they are all there but the league well do you really need to battle the league after becomeing the pokemon world champion
that means you can only fight the gyms after beating the game