As far as I know this has little to do with the file format by itself

MS3D is simple because it has been designed for low poly objects only
It contains information about vetices displacement, bones, U.V. coord etc
FBX include much more information , a lot of them being of no use for game programming

A part from that, priority number one is reliability and FBX is not 100 % reliable regardless of the responsable for the bugs in the pipe line