"Perhaps Marc could comment, as he has both systems."
I'd be glad to comment. In my case, the question would be if I had to give up one which would it be?
I would give up the 503CW/CFV. If buying new, I'd select the H3D-II/31.
The H can be fast, or it can be used slow. The Zeiss lenses can be used on the H, the HC lenses cannot be used on the 503CW/CFV.
The H3D/31 is a 1.3 lens factor ... the CFV is 1.5X ... so the HC/28mm is about a 36mm field of view (wider than a SWC film camera), the Zeiss 40mm is about 60mm field of view.
When we discuss hypothetical questions, and fret about whether something will be around 5 years from now, it's just rhetorical since we need to shoot now, not 5 years from now.
If we want to think in terms of investment, then the answer is invest in yourself as a photographer by getting the tools you need to express your vision. If the tool doesn't do that, don't invest in it. If it does, then that will still be a good investment 5 years from now. There are many working pros using older Imacon, Phase One, Leaf, Sinar and even Kodak ProBacks that are doing just fine.
The Leica S2 is a nice camera (depending on price) ... but it is NOT modular. The 503CW/CFV and H1, H2, H2F and H3D cameras are modular.