I've had dish the last 10 years and had direct for 4 years prior to that. It really is 6 of one, half dozen of the other. Some people get so adamant about which is better, but it's like pepsi vs coke, McDonalds vs Burger King. I prefer Dish, but both have their horror stories and their great customer service stories.
As far as the Hopper, they are pretty adamant about $99 per hopper. If you have the protection plan, the installation is free. I spend a lot each month with them and I still paid the upgrade fee. It's not in my personality to argue for them to drop it, but I've heard some have been successful. There are some good forums on satellite guys.
The Hopper is an incredible system. It allows all TV's to be HD connected, the second tv is no longer sd. The on demand and guide functions are better and much much faster. Each Hopper has 3 tuners and they aren't assigned to a particular tv, you can "hop" between tuners, join the other tv, etc. Prime Time anytime is the best. It automatically records every program on cbs, nbc, abc, and fox from 7 to 10 and doesn't use up your DVR space. It does use 1 of the 3 tuners though. (you can disable this if you aren't interested in prime time tv). At midnight that night each prime time show can be viewed with all commercials removed, known as autohop. (being sued for this). You can now watch your DVR on any tv, pause on one, pick up on the other, etc, the whole home DVR concept. I would suggest if you have more than 3 rooms with a tv to get 2 hoppers. I have 5 tv's , 2 hoppers and 3 joeys. The joeys can switch from hopper to hopper. Each hopper can access the other hopper's dvr menu, but not their tuners yet, though that is possibly in the works down the line. They have already updated the software numerous times. There are many cool features I am forgetting.
In conclusion, it sucks they charge for an upgrade, but I have to say the Hopper and joey system is incredible.