The problem is that the gym meta is basically a CP competition there is not much focus on composition of the gyms.

I would change 4 things.

• Make type effectiveness bonus 2× like in the main games.

• Limit the attacker to 1 pokémon.

• Prestige loss depends in the square of number of defeated pokémon: 1 pokémon would be 500, 2 would be 2000, 3 would be 4500, 4 would be 8000, ..., 10 would be 50000.

• 5 minute cooldown after each attack (like pokéstops).

This means if you find a gym filled with dragonite, you can easily wipe through the entire gym with a single lapras. And raze the whole thing in a single attack.

To efficiently defend a gym when these rules are in effect, you need to use the right pokémon and this pokémon must have the right CP to insert it into the proper place to efficiently defend a gym.

For example an water, ice, water, ice gym is efficient at defending against, grass, fire, and dragon type attacker, but weak to electric. You'll need to insert some ground or other grass type defender to defend the gym against electric types. Given that super effective is 2× non-stab moves become reasonably good and this would make defender to think twice what to put into the gym. And there would be more strategy and more variety in gyms.