The one problem with this writeup is, well, glaringly obvious.
The Shivans basically have jack for what you regard as a worthily written antagonist in the canon, and this is arguably their greatest strength. They offer a great demonstration that in the end, you don't actually have to understand your opponent to stop him, and maybe you can't. They don't have to make sense. They don't have to do the smart thing over the dramatic thing. You don't have to tell the player anything, reveal to them anything. The Shivans simply are, and will always be. They remain as mysterious in defeat as they do in victory. In the end, we're not even sure we know what they want.
Do they have some sort of special exemption clause here? No, not at all. The mystery, the mythology, of a monster is as important or possibly more so than its story. That which you do not understand is far more frightening and hateful then that which you do.