The Card Pool is simply the shared library of cards available to play with in that particular match up.
It is created when both players' Suitcase cards are combined at the start of the game. Each player builds a Suitcase by choosing the 100 cards from their account that they would like to include in the Card Pool.
The cards in the Card Pool will then filter through into the River where players can use the resource system to add any card from the River to their deck. You will end up playing with some of your opponent's cards, and your opponent with some of your cards.
In many traditional games you build your deck before the game starts and only you can use those cards. Synergy of Serra is different, the decks are built during the match up and you and your opponent will use each others cards.
As opponents will be able to use your cards, and you theirs, the development of the Suitcase will have a strategy all of its own and rarely will two Card Pools be the same.