The lighthouse is the gym. When you enter the gym, at that point in the game, did you want to spend 10 minutes or so grinding through trainers and/or puzzles to get to Jasmine? No, because the lighthouse already made you hype enough for the battle, making the gym big would've detracted from the hype and would've been boring.
Another point, is that at that point in the game, all the previous gyms had been relatively big, so when you walk into Jasmine's gym and see it barren, suddenly the hype increases because "oh shit, this is gonna be real".
I think having one of the gyms be empty adds to the suspense because it is unexpected. That doesn't mean more gyms should be empty, because then it becomes expected and ruins the suspence, but, y'know.
