I will explore some more, but one of the problems I have encountered is that the systems I use have different numbers of processors, to eh configuration of NCrunch vs VisualStudio is not portable. Have you considered something like ReSharper has, where there are 3 levels of setting -- System, Solution, and personal? That would be beneficial I think.
However, that is a lot of feature development, so it might not be a priority this year.