The gyms make sense, there are a ton of people playing. What seems backwards is how you claim your coins for being in a gym. You put your pokemon in the gym, then go to the store and you get your 10 coins. BUT, if you put your pokemon in a gym... wait 5 minutes until it is defeated, then go to the store, you get 0 coins. This seems backwards. You'd figure you would get rewarded for keeping a pokemon in a gym, not for doing a driveby on them.
When you fight for a gym, you can't put in pokemon that are hurt. So if you use your top CP guy, he will be hurt after you empty a gym, so you put in a different one. It is better this way, because people pounce on empty gyms. You won't have a chance if you exist to heal your pokemon, then try to get back in. The only time I recommend this is if you are taking gyms with another on your team, so they can enter the gym when it becomes white.