After the Horus Heresy it became very clear that no organization could hold considerable control without the proper checks. Individuals who secretly studied xenos, daemons, and mutants/heretics were around before the heresy, they weren't Ordos until after when the need became apparent.
When Inquisitors first became mainstream, the Ordo Malleus was the all seeing eye of the inquisition because they are stronger in every way than the other Ordos. It made sense on the superficial level because they are trained harder and yea the Grey Knights are the toughest army to date, if or when the Deathwatch comes out then there will be hard evidence to dispute that, for now, I go by the codex.
Mantis said they changed the fluff, I haven't seen any hard evidence, so apparently i missed something big.
As for the Ordo hereticus being the top dog now, it says in their codex they are the guardians of humanity, not the watchers of the watchers. I took it as something to play up the appeal of a new army seeing that that statement applies to the whole Inquisition as a whole. The name implies that they would be but really, isn't that the structure of the Inquisition itself. It's a self regulating organization, the witch hunter codex to me just really reiterates what the whole Inquisition is about, but maybe thats just me.
Hehe, why do i do these things?...the Ordo hereticus is useless, Xenos is cool ..in my opinion. I mean what does the Ordo xenos have going for them, they study and fight xenos and the mighty deathwatch. Which are just marines from chapters with a history of fighting aliens, which don't get me wrong is great, but can't a chapter just fall upon the aliens when the need arises. Ok ok so being vigilant is a good trait, but what would be better is a good few grey knights trained to fight aliens(which they don't need to, but if it makes the idea sound better...).
And as for the Ordo hereticus, they only got critical acclaim because they accused Magnus the Red and he eventually turned traitor. Of course after that it seemed like a good idea to have a whole Ordo based around heresy. Then the whole Vandire fiasco happened and then it was pretty much cemented. But really who can't do the job of the witch hunters. A rebellion- marines, guard, mutants- marines, guard, everything else they specialize in can be done better by someone else, probably not guard but still. They are masters at torcher, talk to the DA, maybe they might learn something. Daemonhunters dont even bother, they get a psyker trained to rip the information out of your head and throw your dead carcass into space. No time wasting with petty cutting and carving, quick and effecient like it's supposed to be.
BUT Who can do a daemonhunter's job, seriously. Who's chamber militant can land on a planet so potent with chaos energy that the atmosphere alone can corrupt their bodies, destroy them or turn them against their comrades? Nobody except the grey knights. SoB and deathwatch can be corrupted, grey knights can't. How many Xenos and Hereticus Inquisitors are commonly known off the top of your head? Then ask yourself how many Malleus inquisitors are commonly known? Every Ordo is based in secrecy, yes, but the Ordo Malleus takes it to a higher level because again they fight the most destructive threat, a threat that would destroy them if their location was known. Therefore, the two other Ordos have little if any knowledge of how to find Malleus bases, this is not so for the Malleus since they have to watch everybody, this ties into the fact that the Malleus uses this to intimidate other Ordos, making them the watcher over the watchers. Apparently I'm drawing on old fluff here so if anyone finds anything to dispute that let me know.
It was so originally, some people say it has changed, there is no hard evidence to dispute it, yet there are superficial, common sense information to show the Ordo Malleus are top dog, so let the rebuttals roll in.