The best thing about going by the Manasarovar Kailash route suggested by MEA is that you have the government’s seal of approval for the Kailash expedition. The route to Kailash Mansarovar is set by a bi-lateral agreement between India and China. All pilgrims get required medical facilities, security and diplomatic protection if they go by this route. You will also get to enjoy the view of the Om Parvat, which may not be possible on other routes. In fact, few selective states offer subsidy to pilgrims who complete kailash yatra. 

Also see Kailash Yatra Subsidy.

However, there are some serious concerns about this Kailash Mansarovar Yatra route because of the long time taken to complete it and the relatively tough trekking that one has to do to reach Mount Kailash. Not all people may find the route a stress-free one. This brings up to the Kailash Manasarovar Yatra conducted by private operators. One biggest drawback in MEA Kailash route is - There is no selection guarantee as all depends on Lucky draw. One can be rejected at last moment too if fails in medical check-up. Many times, Kailash Yatra through MEA got cancelled due to political tension at India-China border. Such issues are not faced in Nepal routes.

For more details on MEA Kailash, Check:

KMY via Lipulek Pass

KMY via NathuLa Pass