I absolutely hate FBX. It is the biggest lie in 3d software.
Remember that FBX is the MotionBuilder scene format, and that’s all it was ever meant to be. Use it as anything more than that- including the utter bullshit Autodesk feeds us year after year about interop- and buyer beware.
Writing a baked file format isn’t hard (and it’s easy to test thoroughly), and until we have a good, open, standard one, I’d say this is one area where I always suggest rolling your own.
I’ve been down this road at 3 games and every experience- widely diverse subjects, believe me- has reinforced my opinion.
First there was getting motion data from a mocap studio as FBX, instead of BVH (which we rolled a loader/dumper for but hey at least it’s understandable). But there was no .NET FBX SDK, and the entire format is undocumented, so no way to roll our own serializers.
Then there was an FBX->XMD converter. It was slow and had intermittent failures. Nothing ever beat our hand-rolled XMD exporter (actually, our DCC->inhouse intermediary-> XMD/BVH/Whatever exporter, could handle all sorts of animation).
Then there were attempts at going between XSI and Maya using FBX. What a mess. Even simple test cases didn’t work right.
There were more examples but I don’t think I need to go on.