Heya,
I'm no audio expert but I like to help where I can. For a remote you might also check out the URC lineup. I have a URC 300 and I really enjoy the touch LCD screen although I realize it's not for everybody.
I found my old Harmony just wasnn't doing everything I wanted it to do via the PC setup. I especially had trouble with components that didn't have discreet on/off codes. Maybe a call to thier support line would have helped me but I'm stubborn.
The URC 300 is totally programmed in the unit itself so be prepared to spend a lot of time programming and rethinking and reprogramming again. But, once you get it the way you want it, you can make absolutely anything happen with just one button press.