As a Person who is interested in Lore i noticed a few "discrepancies" surrounding the Mogu and their new lore from 5.2.
The archaeology description of the Mogu states that a race of brutes stumbled onto the magical powers of the vale, and became bigger and smarter which are now known as the Mogu.
5.2 Lore however states the Mogu were Titan constructs which got cursed with flesh.
Both pretty much give different explanations for the Mogu origin.
Wrathion gives interesting whispers about Mogu / Titan Lore everytime you loot a Titan Runestone (http://www.youtube.com/watch?v=murzhAcDOUE ; They start at roughly 0:50)
It is mentioned that the Mogu somehow were able to reverse the Curse of Flesh, it is possible that they used the Power of the Vale to at least partially reverse the Curse of Flesh, but even with this explanation both sources contradict each other.
Location of the Sacred Mount (Isle of Thunder):
As detailed in http://www.wowpedia.org/The_Sacred_Mount, the Mountain in which Lei Shen found Ra-den, sank during the Sundering while only it's top remained above the Sea, which now known as the Isle of Thunder.
However Ra-dens Encounter Journal says:
"Lei Shen's life changed forever when he stumbled into a dark chamber below what are now the Mogu'shan Vaults. Legend has it he found an ancient titan keeper guarding a miraculous device known as the Engine of Nalak'sha.
Obviously, the Mogu'shan Vaults and the Isle of thunder are at 2 different places.
Also, it is said that the Lei Shen he built a forbidden city atop the Sacred Mount while the Mogu'shan vaults were built as a shrine dedicated to the Mogu Empire, if they were the same place, Lei Shen could have hardly built 2 different things at the same location.
Which would also bring Feng's existence into question, as further Mogu Ruler abandoned the Sacred Mount because the storms seemed to go on a rampage there without Lei Shen.
The Sacred Mount and the Mogu'shan vaults were the same place before the Sundering but were seperated later,though this theory has some holes, it is the only explanation i can think of except a mistake by Blizzard dev's, that would be a rather huge mistake, as 2 Raid Instances would actually be at the same place.
Lei Shen vs. Ra-den
Speaking of Lei Shen and Ra-den, this may not be a huge "discrepancy" as above but rather general question, how was Lei Shen able to defeat Ra-den?
Lei Shen was a strong warrior, but defeating a Titan Keeper is a different story.
In my opinion, it's not logical that this "fight" actually happened under any conditions where you could say that Lei Shen directly fought against Ra-den, Lei Shen couldn't be that strong beforehand.
If you listened to the soundfiles of those Titan Runestone, it is mentioned that Ra-den actually fell silent / asleep and in http://www.wowpedia.org/Lei_Shen_%28object%29 it is stated that "Once Lei Shen had come of age and commanded his own legions, he announced his intent to awaken the gods"
Ra-den itself may not actually be awake or at least in a condition to fight when Lei Shen ventured into the Sacred Mount.
Why Ra-den was asleep (or weakened) is unknown, but Lei Shen maybe discovered how he could claim Ra-den powers for his own while he tried to "awaken" Ra-den
After all, it is never directly stated that these 2 beings fought against eachother, you merely know that Lei Shen took the Powers of Storm from Ra-den and then used Ra-den as his Anima can.
How Lei Shen discovered that Ra-dens Blood can be used to create stuff is a mystery, though.
Twin Consorts Encounter journal says:
"Rumored to be the only known female mogu in existence"
www.wowhead.com/npc=70440 and the associated quest http://www.wowhead.com/quest=32715.
The Encounter journal says that the Twin Consorts are the only female Mogu, while the existence of the Last Mogu queen proves that Female Mogu did exist and Lei Shen killed his own queen for some reason.
Maybe the Mogu experienced something similiar as the Vrykul, that female Mogu gave birth to seemingly "inferior" childs, while the Vrykul chose to kill off the newborn, maybe the Mogu chose to kill off Females which gave birth to "impure mogu" to preserve to impurity of their race?
And Lei Shen then created the Twin Consorts that he will still have some fun, there's a reason why they were called "Twin concubines" on the PTR.
Mogu Procreation & Age:
The Problem of a Race which kills off it's females (or simply lacks females) will have a problem with their procreation, that Mogu procreate the "usual" way can be taken from http://www.wowpedia.org/Lei_Shen_%28object%29.
Young Lei Shen was born the son of a warlord in the terrible Age of a Hundred Kings. Like his brothers, "
If Lei Shen was the son of Warlord and had brothers, it's hardly possible that the Mogu somehow procreate other than Dwarves and Gnomes, which technically suffer the same fate as the Mogu.
As stated above, a Race without females runs into problems after some time, as long as they are not immortal.
The Mogu can hardly be immortal, Dwarves and Gnome live very long but are not immortal, Lei Shen died of old age as well.
But how could Iron Qon be present in the Trailer when Lei Shen's coffin as brought into his tomb as well as Raid Instance?
How could Shan Kien (http://www.wowpedia.org/Shan_Kien) still be alive?
How could so many Mogu still exist if there aren't any females around?
Iron Qon could have been similiar to Lei Shen, he was "dead" and got ressurected by the Zandalari, though Lei Shen corpse got preserved by Titan power, Iron Qon may have been placed under similiar "protection" by the Thunder King.
As far Shan Kien and the procreation thing, i can't think off any explanation.
Shan Kien is an enigma anyway, he tried to hide the bell from the Shado-pan, when those were actually founded after the last Pandaren Emperor.
(= shortly after the Sundering).
It's hardly possible that no Pandaren tried to find the Bell until the Shado-pan were founded, not even focusing on the matter that Shan Kien is over 10000 Years old.
The last thing on my list, the Lorewalker story about the Saurok tells that they used Basilisks which got shaped into Saurok.
However, in 5.2 you learn the the Saurok were created by using Anima.
"Deep within the bowels of Lei Shen's island citadel, mogu flesh-shapers formed the saurok out of a magical substance of unknown origin." (http://www.wowpedia.org/Primordius)
It's a similiar issue as the 1st one, the 5.0 explanation pretty much contradict the 5.2 explanation.
Maybe the "powers of the vale" were used as well, but to reform the flesh created by the Anima, that Anima and the Well were used in conjunction, one shaped the base while the other one was used for the finishing touch.
Or Blizzard simply got sloppy in terms of story telling, that is possibly the most logical explanation for these issues presented above, as i could hardly think that Blizzard could bend story that way that any source is still true while explaining it logically.