I think this is like comparing apples with oranges. It really depends on what you are willing to experience. Lush greenery, beautiful forests, go for Meghalaya. Stark, almost surreal landscape - certainly Ladakh. Weather wise, Ladakh will be much cooler. And lastly, I found the local food to be wow in both the places.
As Leh is getting populated gradually with traveler or backpackers, Meghalaya can be a better option. No doubt Ladakh is magical but one must not ignore the serene landscape of Meghalaya with the lush green mountains and the breathtaking valleys.