I'm aware of this limitation. If you succeed in implementing the node flattening, you'll be able to use the OBJ exporter for more complicated scenes. Thank you for the reminder anyway, it helps me to know what to prioritize.
jReality and SweetHome3D are able to flatten nodes but as their source code is under GPL, I cannot use them in JogAmp's Ardor3D Continuation (even though I encourage people to use the GPL in general).
The Collada importer supports a wide range of features, I assume that writing an exporter for this format will be less trivial than it was for the WaveFront OBJ format. I remind you that the last importer I wrote required between 7 and 14 days of (full-time) work.