If the large pools make a deal, any transactions they don't pick up will only ever get accepted after a very long wait. Hell, since they control >50% of the network, they can simply make the new transaction fees a new rule and force lower transactions to not be accepted by anyone (i.e. ignoring those blocks, like a 51% attack.)
Policy by economic (mining) majority could be an issue in the future when the policy directly determines the profits of that majority.
The behavior of clients does influence fees, but consumers using Bitcoin will happily switch to the client that lets them pay the fee they want to pay (talking about the excess fee not the fee described in https://en.bitcoin.it/wiki/Transaction_fees .)