Until the Hopper is in the hands of knowledgeable people - namely posters, it's hard to compare. And it is possible it will actually have four tuners. (OTA) It appears the Joeys can do everything the hopper does, where the Direct set-up requires you to be recording the program to pause, etc... It also appears Direct TV allows their regular DVR in the system which would provide a backup receiver should the whole house unit fail. The Dish answer may be allowing a second Hopper, which would be integrated meaning all joeys could see both hoppers. Rumor is Dish will not at least at first, if ever, allow a mixed set-up. The direct whole house units do not integrate that way. Already mentioned is the recording of all networks on one tuner, in some households like mine that is a definite plus, some households it may not be.
Because Dish is apparently going to charge a $4 whole house fee, I'm betting the first hopper will not have a receiver fee, as is policy now. You will pay an account DVR fee and the $4 account whole house fee. Then each Joey will be $7, and possibly the second hopper will be $7. IF, that's IF I am correct that looks to be less than Direct TV, especially when the packages cost a little less also.
One last thing I always feel obligated to say, to me the actual content makes the most difference, and on that front nothing has changed much. For the most sports, and in HD (somewhere around 16 to 18) you need Direct TV. Dish has actually improved quite some on the sports front, still lags, but their strong point is non sports channels in HD and movies. If that is more important, Dish is the way to go.