When Pokemon GO was first introduced, the Gym System was completely different than what it is now. This previous Gym System allowed up to ten different Pokemon to be placed at it, being based on Prestige that could be earned and lost depending on who is battling the Pokemon Gym. There was no limit on how many Pokemon of one given species could be placed at a Gym, which was abused by most players with the placing of multiple Dragonite, Tyranitar, Snorlax and Blissey at each and every Pokemon Gym. Because of this fatal flaw that saw most Gyms being almost impossible to defeat, this ladder structure was replaced with the current Gym System.
In the current Gym System, only six Pokemon can be placed at any given Pokemon Gym. Since prestige no longer plays a role, up to six Pokemon can be placed at a Gym without having to battle it in order to open up a slot. The Pokemon will still be battled in the order they are placed at a Gym; however, only one Pokemon of a given species can be placed at a Gym. Since means you can only see a maximum of one Blissey or one Snorlax or one Dragonite or one Tyranitar at every Pokemon Gym now.
On top of this, a new motivation meter structure was also put in place at all Pokemon Gyms. With it, each Pokemon would have an ever decreasing motivation meter after being place at a Gym; the meter could further be lowered by an opposing team defeating the Pokemon at said Gym. If a Pokemon's motivation meter hit its bottom and it is then defeated by an opposing team in a Gym Battle, that Pokemon would be knocked out of the Gym. After all Pokemon are kicked out of a Gym, another team could claim it for their own. In order to make sure their Pokemon doesn't lose too much motivation, players can feed their Pokemon Berries in order to boost their meter. If you visit a Gym and give a Pokemon a berry there, it will gain more motivation than if you are not near the Gym and choose to still send it a berry for it to consume.
Since Gyms are easier to defeat in this new Gym System, players only need to have a Pokemon last roughly seven hours at a Gym in order to earn the now automatic Gym Defenders Bonus. Unfortunately, however, the Defender Bonus has now been reduced to a maximum 50 PokeCoins per day limit. All Pokemon Gyms also include PokeStops now, and it is also at Pokemon Gyms where Raid Battles will take place.