If I had my way, I say keep the old proto because it has the more accurate details especially on the body. Then refine the head sculpt and soften the lines on his nose area so it doesn't stick out as much (should be more like light engravings than being fully sculpted). Make his shoulders sit a bit more flush (like the new proto pics) and finally make the neck thicker.
In the following pic, I only edited the neck for both protos, and it already shows how much of a huge difference it makes:
I feel I should mention that I'm pretty content with the older proto myself as I personally didn't find fault in HT adding the details on his nose area, rather if there's one huge improvement that needs to be made in order to capture Ultron's physique, it's really the neck that needs fixing.
EDIT - Thanks and sorry Brainy. I deleted my post and thought I'd rework it so we can compare the differences.
These are the edited photos by themselves: