Pokemon Go Gyms are populated by only a few Powerful types of Pokemon which are usually the Dragonite, Snorlax and Vaporeon. It just so happens that some of the "lowly" ones can boot out these "champions" from the gym.
Dragonite Counter
There are several counters for a Dragonite but it's particularly vulnerable to Fairy types, according to Pokemongohub. The best fairy fighter of them all is Clefable. Players can get this Pokemon by simply evolving a powerful Clefairy with only 50 candies. Trainers should make sure though to get a Clefable with CP of more than 2300. This is because the Dragonite has a high CP too. The Dragonite also has a typing weakness.
Snorlax Counter
Many Pokemon Gyms have Snorlax defenders due to their huge CP. It's not particularly effective though against a Beedrill. This Bug type Pokemon is actually the third evolution that started from Weedle to Kakuna to its present form. It's Bug and Poison combo type too and only takes 62 candies to evolve, according to bulbapedia. Compared to the Snorlax, the Beedrill can only managed to obtain a maximum CP of around 1770.
The Snorlax is not a pushover but it could not deal big damages to Bug, Poison and Flying type Pokemon. Unfortunately for the undisputed gym tank, these are the three qualities of the Beedrill. Ironically, the flying bug can simply wear down the Snorlax in gym battles.
Vaporeon Counter
Vaporeon is also the one of the best gym defenders out there. It can be defeated though by another common Pokemon - the Parasect. In the CP department, this bug type is quite weak with only around 1650.
It can defeat a Vaporeon though with much bigger CP. What Pokemon GO players have to do is to take advantage of its Moveset superiority. It seems most Pokemon with Solar Beam can defeat a Vaporeon despite its vast CP reserves. So far, the most common and easily obtainable Solar Beam equipped Pokemon is the Parasect.
Pokemon GO has its ups and downs but it's clearly evolving albeit slowly. There is also the possibility that breeding will happen soon due to the introduction of male and female genders.