Most of the time Dish will waive that 29.99 fee. The other thing is there is no need to pay the 4.99 a month. Most people on here will tell you that if you have a problem you call and put it on your account. Then call back and get the service call. It's not like you should need service very often if it is put in correctly.
I am sure others will have more on the advantages, but here is what I see.
Dish has dual tuner dual tv receivers. Much more flexible in certain applications.
Less money for Dish with equal systems. You only have to pay for 1 receiver on a 2 room system or 2 receivers on a 4 room system, if you can get phone lines to the receivers
Dish DVR's are better units.
Direct has more HD channels at this point, but that does not really mean they have more HD. Just more upconverted SD. This is going to be a back and forth thing between the two as more system upgrades and channels come on.
If you are a sports nut Direct has the lead here, but you pay for it.
Alot really comes down to what you find more important. They are pretty equal for the most part. Service is pretty equal as well, just depends on where you are.