The Duo is an excellent box and still is. If you have no need for further tuners nor plugin tuners then you really do not need to look that much further.
The Ultimo is however a fantastic machine and very flexible but lets be honest a lot of people have and are still pefectly ok with a single tuner machine. In that respect the Duo is still way ahead of the pack by having two.
The hardware on the Ultimo is certainly impressive and the faster processor is great but the Duo is no slouch by any means.
On the physical side of it, I would actually say that the Duo is the better built machine out of the two. The quality of the casing and build overall for example appears to be marginally better than the Ultimo.
You also have the remotes. Ultimo's remote looks fantastic. This of course is a personal preference but personally I find the Duo's remote more comfortable.
The Ultimo is of course a beautiful looking machine. The OLED VFD is stunning and the touch sensitive buttons on the front panel give it some class.
Of the two the Ultimo is the better model but the $million question is, is it worth all that much extra ? Once again this is personal preference as the Duo is a high end receiver and in itself miles ahead of anything else on the market.
I think when you get into comparing machines and specs then you can get drawn into all sorts of equations and lose sight of what it is you are trying to achieve. When it comes to Linux receivers then it can become a blur. The Xtrends/Clarkes are also very capable machines.
If you are going for a Linux machine then I would certainly say build quality should be one of your key concerns. All these high end receivers are in actual fact simply Linux PC's converted into set top boxes and you really have to consider things like PSU's, cooling and quality of components.
Enthusiasts do consider these elements seriously as they tend to use their machines extensively and for extended periods of time, which is where quality eventually tells.
At the end of the day I would say out of the Uno or Duo, at current prices I would certainly go for the Duo. Out of the Duo and the Ultimo, it's a price thing and how flush you're feeling. You won't go wrong with either.
For the record I have both Duo and Ultimo.
Hope that helps.