In any TCG, there is a balance: action - counteraction. Because of the way Pokemon TCG functions we can't activate trap cards or throw an instant on the stack to react to an opponent's effect, but we can set up defenses. For every effect that does something, there are effects that counter it. For example:
there are effects that increase damage - there are effects that reduce damage or heal it afterwards
there are effects that apply status conditions - there are effects that remove or prevent them
there are effects that deal damage to benched Pokemon - there are effects that prevent damage to the bench
However, there is a definite imbalance in this game, such as...
N or Red Card - there are no effects to stop an opponent from shuffling your hand
Mars or Delinquent - there are no effects to stop an opponent from discarding from your hand
Field Blower or Crushing Hammer - there are only a few effects to stop an opponent from detaching cards from your field and none are practical for general use
Escape Rope or Lysandre - there are no effects to stop an opponent from swapping your active pokemon
Durant or Houndoom EX - there are no effects to stop an opponent from milling your deck
When imbalances such as this exist and have not yet been fixed, people take advantage of the situation it is known as an exploit. That is what the OP faced: an exploit deck.