The social structure of steppe peoples was beginning to change dramatically during the time period covered by this game. Previously the plains extending across Northern Eurasia had been dominated by mounted nomadic tribes organized into a military hierarchy. This had allowed for the rapid expansion of the Mongols and other steppe people, darting from one end of the continent to the other, descending into and pillaging the settled agrarian societies on their periphery. But as the plains themselves became increasingly settled, and local populations turned from reliance on grazing animals to subsistence agriculture, the days of the nomads inexorably came to a close.
Were a fantasy Mongol scenario to be created, it would have to be set early in the game's timeline - it would basically be a race against expanding Russian civilization, as the latter established settled agricultural communities. At the same time, other steppe societies, particularly those that established themselves along Central Asian trade routes, would have proved a more formidable opponent to Mongol expansion than did the relatively weak and divided tribes of the 13th century. Perhaps fantasy events could facilitate Mongol advance across southern Siberia, but it would be unrealistic to give them too large an advantage over the Central Asian countries, as does the Mongol Fantasy Scenario.
Another possibility would be to allow for the Mongols to take the place of the Manchus and overrun China during the early 17th century. But it would definitely not have been possible for the Mongols to "replace Kublai Khan" and take on the Ming Dynasty during its height. All Chinese dynasties go through a cycle of ascendance and decay. Their collapse inevitably occurred only when the hydraulic infrastructure built earlier in the dynasty began to fall into disrepair, setting the state bureaucracy into conflict with the local notables in an attempt to secure labor power. This was a non issue in the Ming Dynasty of the 15th and 16th centuries.
There is some interesting potential for a Mongol Fantasy scenario, but many more limitations than have been posed by past Fantasy scenarios. I would not say that all the work required to get this right would not be worth it, but there may be other scenarios that would be more interesting and easier to create first.