It definitely matters when getting the agent to accept a contract offer, and I've used this to my advantage as well. But I feel like once the offer has been accepted by the agent, and the player is considering a number of offers that his agent brings him, the agent fee should be taken out of the equation. I was waiting to sign this 4-star player on free transfer all season, negotiated a deal with an agent right on June 1 (England), but the player rejected it, one of the two reasons being that HE felt that HIS AGENT's fee was too low. Mind you, the agent fee was higher than what he asked for.
I guess IRL, the agent, being the selfish bottom-feeding creature that he is, might try to sway the player to take a deal that benefits his own interest...but I would think he'd at least do so under the guise of more legitimate reasons (club stature, playing time, etc.), and NOT his own fees. And I certainly can't imagine a situation where a player would actually state that his agent's fee is too low in rejecting a contract, these players must really love the **** out of their agents :S