The arable parts of what used to be Mongolia are largely majority Han nowadays and have been for the better part of the twentieth century. This a big chunk of what is called "Inner Mongolia", which is a province of China.
The parts of Mongolia (both Inner and Outer) which are still Mongolian are, on average, the more arid ones.
It is true however that Mongols are more numerous in Inner Mongolia than Manchus are in Manchuria. It may be that part of it has to do with a later and less sustained Han settlement, but I'd say the main factor is that a large chunk of Mongolia is quite barren, especially if compared to the fertile, relatively well-watered, resource-rich Manchurian Plain.
So, two factors primarily:
1) Mongolia is a desert. Where it isn't, it's often not much Mongolian anymore.
2) There was a thing called Red Army, that guaranteed Outer Mongolia's independence from China, thus preventing any significant Han settlement there (which was relatively unlikely to begin with due to the aforementioned fact of it being a desert).