I just beat the prototype
It seemed to me that cards going into the discard pile immediately after being played to the line gives the player a bit of an advantage, or at least presents the opportunity for abuse. It made it a lot easier for me to win by getting multiple leaders on the line even though I only had one in my deck.
That an interesting point. I'm not worried about advantage since I see that being part of a strategy. And I don't see yet how we can abuse that. To get the leader second time we still need to cycle through whole deck first and then draw it again. That should take at least couple turns usually. And that's not much different from CCGs where you allowed to have multiples of the same card.
And I like this way of doing things because it's very transparent and allows for very small player's decks. If we would "lock" used cards on creatures until they die we would only have enough cards to create 3-4 creatures with a 10 card deck.
That being said I don't think that the current system is perfect and there are probably ways to refine or even completely redesign it.