I know I may be saying something obvious since I've been gone from the expansion since the launch but I noticed most guides here do not mention it.
I noticed that it is very possible mote of harmony has a special internal cooldown of probability to drop. My first reaction was that "nah, it's just in your head, RNG is playing tricks on you", but the occurrence of the phenomenon is too common to avoid noticing.
For example, the most blatant examples: Fly around for 8 minutes and then kill 1-2 lowbie mobs, 1 mote of harmony, then find 5-6 or more mobs kill them, 1 or 2 motes of harmony, then nothing on the next couple and then you pull a humongous amount, more than 20 and you get again 1-2 motes only, and it goes on.
It's as if the algorithm is not simplistic but it works like that with diminishing returns: "give him a chance of that #% to get a mote, however, diminish his chance incrementally (and never zero it to not look totally fake) to get more than 2 or 4 in the same pull, but then increase his chance progressively as the time goes by".
In case anyone thinks Blizzard isn't into algorithms like that, I urge to google of their official interviews' remarks that at least some quest items (of not important quests at the time) do have "rigged" chances on purpose (e.g. "if he doesn't get the 10th of 9/10 items after 8 attempts, what the heck, just give him a huge chance to not frustrate him".
By the way, why I believe this is happening. I have a theory that is my only one and it makes perfect sense to me: The very reason of existence of the item, is also what would drive them to do it, make main characters play mainly (I'm sure most of you here, as me, were frustrated at first seeing their alt professions being handicapped by it), so that this internal cooldown/diminishing return system would make it more rewarding and natural to progress in professions and gold via a main character, more time played leads to more motes gained, not just roll a warrior that you never played, pull 200,000 mobs in 2 minutes and call it a day, you'd have to play it, and that algorithm would ensure it.
I was thinking, it may be tied to the initial mass-loot changes at the launch of 5.0. There was a lot of nerfing of items like cloth, but what most didn't speculate, was that it may be tied to the single pull or not. i.e. there may be higher chances for a mote on 10 pulls of 1 mob than 1 pull of 10 mobs of the same type. I'm sure many have noticed it.