I have a 2006 R350 with Nav can I buy and install a newer COMMAND unit?

Thanks

I assume you are talking about the new HD based navigation.

Longer answer is "yes, anything is possible if you don't mind to spend couple thousands".

Shorter answer is "no, it is not worth it for the money".

Is there any other year that easily and cheaply could replace the older COMMAND center in the 2006 R350.

I looked into this for my 07 R Class which has the same command that you do. It's a lot of work and a lot of components are involved. It also depends how deep into the system you want to go (bluetooth, backup camera, rear seat entertainment?). For the basics you need a new head unit, wiring, and the amplifier. Then if you want those other features like bluetooth, backup cam, rear entertainment you need all new pieces including a new rearview mirror. Then you may or may not need a new steering wheel so the buttons will work with the command. Basically more hassle than it was worth for me especially since I wanted all the bells and whistles that my system already had.

There are only two versions. Is it something specific you want from the new COMAND?

If your car hasn't harman kardon , there is no problem for the upgrade. You need the new comand and a new microphone. Bluetooth is included in the new unit. You need someone with stardiag to activate it. The rear camera, if present, is compatible . The rear screens are not compatible.
If you have harman kardon as my car, you need to buy the 2 new amplifier instead of the one now present. The conversion cables don't exist. You must made it ..
In Italy there is a friend of mine very expert in mercedes upgrade . www.mercedesmods.it . He is vice-president of the mercedesbenzclub . I'm a member of the amg staff.