As far as I know this has little to do with the file format by itself
You miss the point, maybe i was unclear. Why should i go the extra route across the Milkshape format when my 3D package can export to FBX and this is a working pipeline? Even more when by Milkshape some of my informations gets lost because its format is a bit too simple here and there ...
FBX include much more information , a lot of them being of no use for game programming
And what exactly do you mean here? Name me one