Well the remote sucks, that’s for sure. But don’t all remotes shipped with devices suck? I use an MX 850, and I would bet most HT owners also use some sort of programming remote so this topic regarding the Marantz doesn't get much traction that I've noticed.
Not sure why you would want to cycle through HDMI inputs anyway, that would be a time consuming headache. Every time you do, you’ll be forced to wait for each device to acknowledge that they are compliant, give a quick handshake and then allow the signal to pass. I’d much prefer to have discrete commands.
Not sure about the report that you have to have non-used HMDI sources off either. I have three and they are all powered on and off when I fire up / shut down the system. I have not noticed any undesirable symptoms from doing so.
I have a "switch" button set up on my 850. It has macros that configure each devise with one button push.
Maybe you should consider picking up a new remote?? If you go to Surf Remote .com and give Mike a call, he'll hook you up with one that will fit your needs. Don't let the advertised prices scare you either. They are not what you will pay.
http://www.surfremotecontrol.com/
I've had this reciever for a while now. It's not the easiest to set up, but it definately isn't the hardest either. It is loaded with unique features that are somewhat obsure to find. When you run up against somethign weird, just ask.