I agree it is hard to compare. Both have the Buddhist atmosphere, with payerflags, Temples and Monastries, but they are different too.
Mustang in north Nepal can be reached by walking several days up and down, crossing valleys from Jomson north,It is possible to reach Jomson by flying from pokhra which can be reached from Kathmandu by road or flight. You'll need a licenced guide, minimum two people in your group, and pay for a permit of 10 days.
Most Monastries are deserted and the Temples not in a good shape, it look's like no restoration was done for a long time. Ladakh, in the northwest of India, can be reached by a roadtrip of several days, or by plane. As it is at 3500 meters altitude, the first days should be used for minimal physical activity in order to acclimatise. In Ladakh you can drive, visit monastries, and after you're acclimatised, you can do walks or treks. These can be organised locally, there are many local travel agents, of course some market and many hotels and restaurants.You'll see more tourists in Ladakh than in Mustang as it is easier to reach. If you want to visit mustang go in tiji festival time which was in may,and permit cost's around 500$ for 10days