I have had both and I LOVED the MX800. But.... when I set up the Harmony 688 my wife and babysitter both stopped calling me at the office for "tech support."
The MX remotes are awesome and easy to use when you are the one who set it up. You can also put in a little extra time and effort to make it easier for others to use but for some reason it is still intimidating to the non-geeks in the house.
My two cents...
Get the MX if you don't mind the set-up process and tweaking and if you are constantly tweaking the advanced settings on your home theater. Both remotes are equally capable but I found the MX remote to be more capable setting up advanced commands. I also prefer the "feel" of the MX remote. It's a little more substantial so it must be more powerful, right? ;-)
Get the Harmony remote if you want a quick set-up and don't want to take the time to figure out every Macro permutation to power on devices or switch between viewing modes. Or... if you're forced to share the remote with others.
Truth is, you can't go wrong either way!