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One relatively large issue we have in freeCAD at the moment is that we can't export more than one mesh object at a time.
This is bad, because the only way to assign properties to elements that I have gotten to work in freeCAD is to do so to FemMesh objects.
If you had, say, a part with more than one thickness to it, or even an assembly with more than one part, or even two different types of elements, you can't really get any of that info out.
Another MASSIVE problem is that FreeCAD can't import something, and then export it without changing it in an unpredictable way.
Namely, FreeCAD changes the IDs of every single object in the mesh when it imports it, and then changes the IDs again, in a way I don't fully understand, while exporting it.
This may be off topic.
One thing you may be elated to know is that nastran has the best open source reader that exists for any FEM solver I know of; pynastran, maintained by another mystran developer named Steve.
https://github.com/SteveDoyle2/pyNastran
Pynastran is the best bdf reader/writer out there; better even than the enterprise tools that exist in some ways.
We'll be using pynastran in the FEM workbench to my knowledge to deal with some of the bdf files strangenesses, so it may already be in FreeCAD! This would theoretically make bdf files easier to write than calculix inp files