Apparently we don't play the same game because in the current state, it is already pretty fast as it is to get geared. If they actually did implement what you suggested, then you would see a whole new slew of player complaints asking for even more content because they have nothing else to do. With the way it currently is, you do have to do multiple runs which takes time to gear your player out which is a good thing. There is no reason to get fully geared within 1 month of the release of a new raid.
So you actually think ninjalooting is a natural way of progression? That the DEVs has taken into account that a certain amount of items will be "lost to ninjalooters" and therefore it is part of the progression?
It might work for the first character, or the second or perhaps even the third but when you have like I have for example 16 characters (10 level 50:s), you hardly appreciate doing flashpoints over and over again simply because a player decide to take stuff they have no business taking.
That is why bosses drop randomly out of a "boss pool of items", that is the reason to rerun a flashpoint. Not because a player has ninjaed a item, that creates much more frustration then needed. Hundreds if not thousands of posts and many threads prove my point here, just do a search.