I mostly use OOo.org, but when I needed to produce scientific grade
figures/diagrams I found OOo.org weak. I stumbled upon the application gnumeric
which according to me provides the user with the outmost control when editing
diagrams.
 
In short, make diagrams editable in an "advanced" way along with the traditional
way of editing. There could for example be an "Advanced edit" option when you
right click on a diagram. This option should present the contents of the diagram
in the way gnumeric does. 

What gnumeric does is present all part of a diagram i a kind of tree-like
structure, probably based on the underlying xml for the diagram. Here you can
add, remove and control almost every bit of the diagram. It can be somewhat
slow, but your in total control. I doubt there is more functionality in
gnumeric. It is just the way you can access the functionality I really like. 

I find that calc is not very intuitive when editing diagrams. I find I need to
click and double click in and out of diagrams a lot to access different parts,
and I find it difficult to actually remember all the steps. A friend of mine
swore you could not add trend lines in calc, but of course you can. You just
need to double click in the diagram, then double click on a data-series in such
a way that the data-series is selected and not just a single point. Then right
mouse button... And if you miss one click you need to start all over again by
clicking outside the diagram...