I tried looking at the svg side and I'm a little confused.

How about, as a first step, modifying inkscape so that rulers and mouse pointer 
coordinate status use the origin that is indirectly defined by the viewbox? 
What about the viewbox units? Second step would be a gui to actually configure 
the viewbox within inkscape in a user friendly way. Finally, using those 
coordinates directly for new objects instead of inserting another 
transformation (I think this is what Krzysztof wrote in the previous post).
(viewbox reference: http://www.w3.org/TR/SVG/coords.html#ViewBoxAttribute )
I played around with a hand coded svg, in case anyone else is interested I 
attached it.

This alone does not allow setting up an inverted y axis (to enable having y 
axis pointing up like now) but it looks like there is a ‘svg:transform’ 
attribute for that. Inverting the axis would also require things like flipping 
text, I think?
(svg:transform reference: 
http://www.w3.org/TR/SVG/coords.html#SVGGlobalTransformAttribute )

Maybe it helps if we can agree on how coordinate systems should be defined in 
the svg and how inkscape should display units and rulers?
I feel like I haven't really understood all issues.

** Attachment added: "viewbox with origin in the center of the page"
   
https://bugs.launchpad.net/inkscape/+bug/170049/+attachment/3551689/+files/viewbox-test.svg

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https://bugs.launchpad.net/bugs/170049

Title:
  Inverted ruler co-ordinate system

Status in Inkscape: A Vector Drawing Tool:
  In Progress
Status in “inkscape” package in Ubuntu:
  Triaged

Bug description:
  The y-axis of the rulers' co-ordinate system is
  inverted (increasing upwards), and places the origin on
  the bottom left of the viewport. The SVG spec places the
  default origin on the top left of the viewport, and has
  the co-ordinate system increasing to the right and
  downwards.

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