Cards are banned because in the given format they are to powerful, not fun, create unwanted situations etc.
The card can achieve this effect by its own (see
Jace, the mind sculptor) or in combination with other cards.
Ponder falls into this category. In standard its interaction with other cards is acceptable, why in extended there are a lot more cards, so there are a lot more interaction, some...unwanted.
This is a general explanation of bannings, hope not too trivial for you