There's a win win here. Instead of increasing fees at the protocol level by increasing the minimum relay fee or block inclusion fee, you can raise default fees in whichever wallet you wish to market, and send them wherever you want. The web wallet already charges non-network usage fees per transaction to pay for development, and modprobe's light wallet is also already designed so that anyone can run a light server, and charge additional transaction fees to the users who use that server. With slight modification, any light wallet should be able to send transaction fees to the address that payed for its account registration, or to the first account they received from, or whatever other method is chosen to designate a referrer account.
Protocol level changes are less flexible and more controversial, and should be avoided whenever a solution exists at the application level.