The main characters are not amazing in any way; little do they know that the league challenge they participate in is actually a junior division. This explains why Leaders who have been doing this shit for years are using lv 30 shit 'mons of the same type.
Cheren even bitches about this in B2W2, until Juniper pretty much explains that he can't use his "real" team against newbies because of the obvious power discrepancy. This theory is also addressed in ep 120 of the anime where Team Rocket tells Casey that Ash was effectively cheating for using his Charizard against her. While this becomes suspect since Team Rocket is the source of information, there have been no other attempts to confirm or deny this.
On the subject of evil organizations: The biggest obstacle for the theory is how a fucking 10 year old runt defeats terrorist/criminal groups with such large numbers. Simple, as another anon pointed out: the evil teams are not composed of trainers; but of thugs, terrorists, corporate types, and smugglers. When the biggest goal of Team Aqua/Magma is eco-terrorism, large scale heists, excavations, and demonstrations, that leaves little time for actual training. This is one of the few instances where the young age of the trainer is a boon, they are in a developmental stage where they can absorb knowledge and skill faster than an adult. (Think of how adults bitch about 12 year-olds on Xbox beating their ass, those 12 year-olds have nothing better to do than play all day and learn the system.) The main characters have been doing nothing but battles from the time the game starts, of course they will have an advantage over someone who doesn't battle constantly.
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