I am trying to figure out how Blender could be used in complex data plotting. There is no specific need now, but often I am asked how to plot multiple series of data. Read data from files is pretty simple, a little harder is to plot axes and scales, legendas, etc.

Anyone has experience with this issue?

Pretty easy.
You can actually create meshes from python script.You can also set materials.You can plot the scientific data.I donno what kind of plotting you need but one thing for sure is that you can customize blender to your requirement via python.

Easy...I am usually not so optimistic

Several aspects must be considered. Thinking about plotting multiple series of x-y data, we have to choose the datapoint type (small sphere?), how to construct axis and automagically scale them with data range, how to choose illumination and camera position.
But yes, I think blender gives a lot of opportunities.

I will first try to 3d-plot nuclid chart (isotopes, binding energy, etc).

Contributes welcome.

Please let us know if you make any headway with this. I need to be able to make dynamic plots in the game engine. Say, in your game you have a falling ball.. I will need to plot speed / acceleration / position vs time ... etc. as the falling ball moves.

Will keep in touch.

Slugzzz

This isn't "blender" specific but http://www.gapminder.org/
has a really good way of doing plots.

Probably what you would want to do is scale your data to
values 0.0 - 10.0 or something similar, have a fixed camera and lighting
and then if you get additional data, rescale things as they go
If your doing it "realtime" allow it to go X amount over the scale before you
adjust things to again fit in the 0.0 - 10.0 range.
(make sure your camera can see the data that goes outside the optimal scale)