When you add a third party to any transaction, you inevitably add a cost that the buyer ultimately ends up paying, in one way or another.
I'd love for hotels to pass along their commission savings to guests who book direct, but I can't see that happening in the foreseeable future. Right now, if you're a Diamond/Giraffe/Platinum Guest or whatever high level with a particular chain, you'll get benefits on your booking that you wouldn't have otherwise have gotten. But if you're a Platinum with Marriott and a Diamond with Hilton, but have no status with Hyatt, what incentive do you have to book directly when you want to stay at a Hyatt?