The Mogu seem to be a pretty decent point within the MoP Plot, there some things known about their past and that they have Titan relation, but their actual origin is pretty much a mystery.
Personally i've wondered much about this, i think i've came up with a possible explanation.
Mogu are Vrykul who encountered the magical fountain within the vale and got transformed into Mogu.
At first, it sounds a bit odd mostly because Vrykul are a race that mostly appeared in Northrend so far.
The Similiarities between these 2 races are pretty big.
1.They both have a relation to the Titans
2.Mogu and Vrykul frown manual labor, prefer to use slaves for their, the Mogu even had magic at their disposal to build stuff but they used slaves instead
3.Both favor large weapons, appear very xenophobic and arrogant
4.Favor of Rune Magic
5.Mogu live in Clans but have a single Emperor / King, like the Vrykul
From a timeline perspective, this is possible as well.
Vrykul are an ancient race, if not one of the 1st races created by the Titans, the Mogu are very old as well (1st records start at 12.000 years ago)
Now, let's say a few Vrykul travelled by boat (I mean, Kvaldir were already around Azeroth before the Sundering) to Pandaria and encountered this fountain.
Last indicator is this NPC in the Shrine of two Moons, Ruben Holen, his flavor text may support this theory.
"These Pandaren are sittin' on a treasure trove. They even got books in here about vrykul. I mean the vrykul! Come on! How could they possibly have encountered them?"
The only thing that i can't explain is that their body structure is highly different, mostly their legs.
However, this Fountain may change some physical attributes, the Jinyu do not share much physical features with the Murlocs, but are confirmed descendants of them.
Last fun note at the end, Mogu have your mother jokes:
Your mother is so old, she saw the rise of the first kingdom!