First of all i'm kicking myself waiting for the NatAmi to finally arrive. When it does i am going to buy it without a second thought 
There has been lots of talk about the hardware of NatAmi but nothing about what it will run on. Which Amiga os would be the most ideal to use?
Seems a bit premature (to me) for you to be wondering this. The Natami doesn't exist yet in a form we can buy and may never exist (hopefully it will, but I never believe any hardware announcements in Amigaland until I see it for sale).
I really wanted to buy a Natami in 2008. I was hoping my Amiga would last until then so I could switch over to the Natami. By 2008, it had been several years since it had been announced and the first Natamis were supposed to be available that summer.
My Amiga did break down that year, the Natami wasn't around, I was forced against my preference to switch to a Windows box running WinUAE.
But - then I discovered that emulation was not the devil I had thought it would be - it was actually an AWESOME Amiga experience! I could do all the processor and memory intensive productivity work I wanted to much faster and much cheaper.
Still, if the Natami had been around in 2008 things would have played out differently and I would now be a Natami owner.
I might still buy one if they are cheap enough. I support the idea of making a 68K based Amiga clone with enhancements.
To answer your original question, I think OS3.1 or 3.9 would be really what it has been designed for. Hopefully the AROS kickstart replacement will be available by then to make all things nice and legal.