I can see the lack of a dual tuner on a single Hopper being an issue. This is one reason I prefer the Genie/HR-34 install and setup which allows for a dual tuner OTA add on. Problem is I prefer the Dish GUI, HD lineup, and Hopper features. Did you verify your software version is up to date? Keep us posted on any issues or if you resolve it.
The Genie can't begin to compare with 2 Hopper system. 6 tuners (plus PTAT) plus 2 OTA Additional
tuners. For the difference in overall service cost you can add a Joey ($7mo) next to a Hopper and with a simple HDMI input change, have access to all
tuners, timer setting, and all
recordings from that location. Far more storage space, more timers and events, a truly versatile EHD arrangement and a far better interface. To me, the only reason to even consider the Genie and suffer through its problems and limitations would be the sports packages. Fortunately for Genie users DirecTV allows you to keep other HD DVR/receivers in addition to clients to ease some of the limitations.
Now back to OTA for the Hopper...