"Discussion is ongoing whether to devise alternate uses for guild tokens or do away with them completely. In the case of the latter, we will provide players with a means to exchange their tokens for gil, company seals, and items. Details will be announced pending finalization."
I don't really feel guild marks add anything to the game and I will be pleased to see them go in favor of a better reward system. However, I would like to suggest that no matter what system is chosen that anima be added as a possible reward.
To date, there is no way to replenish anima except by waiting. While the addition of airships and chocobos have greatly eased the inconveniences of the player, it can still be remarkably tedious to get around to certain areas once they exhaust all their anima.
A very active player who is completing many different quests and constantly doing guildleves in different camps will be wasting a colossal amount of time traveling. And once a player runs out of anima, the game essentially becomes a travel simulation which only takes away from the main purpose of the player, whether it's completing missions, quests, or looking to exp. A lack of anima creation will eventually erode at any active player's incentives to even pursue their goals. Rather than a question of "what should i do today?" the question instead becomes "is it even worth it to spend the time traveling so i can accomplish my goals?" Or perhaps more specifically: "is not wasting my time worth more to me than my goal, because if it is i won't pursue my goal." This inherent balance is a huge problem and a game shouldn't force you to weigh the balance of enjoyment versus apathy.
Having anima rewarded as either a replacement for marks upon completing a leve or as a choice of rewards would greatly smooth out the player's gaming experience. By giving a player more direct access to the things they want to do that player, in the end, will be able to play more, enjoy more, and accomplish more than they would without these conveniences.