It is my opinion, as a game designer and consultant, that the Gym Meta is fundamentally broken. Understand that when I say that the meta is broken, I'm not talking about the power level of specific Pokemon. I say it's broken because it doesn't accomplish the goal it set. The way that gym defense is set up, it doesn't fit well into the player's ideals of overtaking and maintaining gym control. The system we currently have is O.K., but it's not great. There's great ideas that need refinement or finishing. There's potential for more. When I initially wrote this post, I had paragraphs explaining my case. I decided that the post was too long, and have grossly oversimplified it.
There are three reasons to take a gym and hold it for an extended period of time: to earn your daily coins, to gain more balls from a raid, and for fun. Most of the player base is casual, not needing coins or extra balls. Competition for gyms is low, so gym defense defaults to one team holding it overnight while another takes it in the morning. With this rotation established, players don't need to invest into proper defenders beyond a single Blissey. In all but the most competitive zones, earning coins can be done with your lowest CP pokemon. This is not the case for every gym, and is especially untrue in dense cities, but it is the case for most of the playerbase.
This system is not fun. It turns gym control into a daily task that requires no thinking or finesse. It's not the way you tackled gyms in the main series games, and it's not what players wanted from the game. We already have daily catch, daily pokestop, daily raid, and daily research, do we really need another daily quest? Pokemon GO doesn't need the gym system to entice players to play, players already like the game.
So what would make it fun? What would make the gym system more entertaining or exciting? What would make the system more competitive for otherwise low-traffic gyms? I think I know the answer, and I'll explain it in detail.
For me, the fun of taking and holding gyms is the metagame. Each Pokemon has a type that describes their strengths and weaknesses. Furthermore, some Pokemon learn moves outside their typing. This creates many permutations of optimal lineups. Once your gym has a Blissey, which pokemon fill the other 5 slots? As an attacker, the fun is analyzing the lineup and determining the most efficient way to dismantle the defense. There are no shortage of generalist attackers, but maybe the lineup calls for some off-color specialists.
My idea is simple: increase the rewards for holding a gym, and optimize the timing for convenience.
#1: Coin Collection occurs every day at 4am. Regardless of your Pokemon occupying the gym, coins are dished out automatically. You earn 1 Coin for every 10 minutes per Pokemon that occupied a gym that day. I think 4am is optimal, to ensure players are not giving up sleep just to have a shot at in-game currency. By automatically dispensing the coins, players do not have to wait for someone else to knock them out.
#2: Players earn items for defending gyms. These can be as simple as normal Pokestop items, to rarer items like Rare Candies, TMs, and Incubators, or even cosmetics. These are also dispensed at the end of the day.
#3: Players are rewarded for taking control of a gym. If you take down a gym that you have been to before, you will only earn this reward once per day. If the gym is new to you, then you may earn the same reward again. Again, these rewards can be in the form of items, stardust, or cosmetics.
All in all, the goal is to encourage players to get excited about holding gyms. The general idea is to encourage long-term gym defense, exploration, and interaction. I think this is the system most players had in mind when the game was released. I think this is the system players would prefer.