There has been some discussions about adding variables and counters to the system. I would recommend a small adjustment to the already existing deck system.
Let's say you want to keep track of how much money, mana, whatever each character has. You could in theory already do this, by making money or mana cards and dealing them to the players. However, this system doesn't work really well, because you can not easily split your hand and trade a certain quantity of cards. So I suggest a modified version of a deck called a pool.
Where a deck is a collection of different random drawn cards, a pool is a collection of identical tokens (not like the tokens you put on the board). When the DM makes a pool, he gives it a name, uploads a single picture (like the back of the card deck) and specifies how much units are in the pool or if the pool is infinite.
Just like the card deck, pools can be shown or hidden. You can then deal units from this pool to a player hand. Just as with cards, everyone can see the number of units a player has in his hand. Unlike with cards, this number could possibly even be a decimal number, if the DM allows it.
When the player clicks on his unit hand, he should easily be able to stack and split his hand into piles. This stacking and splitting ability constitutes the main difference between the card system and the pool system.
Players can steal or trade amongst each other, place quantities of the pool on the table for anyone to pick up or return units back to the pool. You can already do this with cards, but since it is difficult to select a quantity of cards, the system would benefit from this change.
PS edit
I just found that someone had a simular idea here, but that thread appears to be closed now.
<a href="http://community.roll20.net/discussion/161/multiple-card-copies-in-a-deck/p1" rel="nofollow">http://community.roll20.net/discussion/161/multiple-card-copies-in-a-deck/p1</a>