I had several Harmony remotes when they first came out and they were not very satisfactory. I'm surprised to see so much acceptance now. They were painful to set up.
I can't say if the process is better now since I'm a new adopter, but once programmed you never have to touch their software again, unless you're adding a new device.
I think that having the touchscreen on the Elite helps, as it tells you what the remote is doing and gives you access to the full list of commands for each device should you ever need that, even if you don't have them all assigned to physical buttons.
I can't think of the last time that I used direct device control though.
I actually only use a single activity on my remote 99% of the time, now that I've got it programmed right.
Activating it sets up all my devices (power on, select the inputs etc.) and then I have commands assigned to the physical buttons spread across all of the devices, covering the necessary commands.
I was actually mistaken in counting the number of remotes it replaced, forgot that some of these devices even
had remotes because I bought them after the Harmony.
Attached is an image detailing the activity that I use most of the time.
Edit: the mute button is also direct DAC control, not a Media Center command.