If inner Mongolia was united with outer Mongolia it would only make it a stronger country. It is hard when parts of a country are not united. Unification is almost always a good thing, and this is definitely the case for Mongolia. I would love to see inner and outer Mongolia united.
Mongolia should be unified, if the people in the two regions desire unification. But areas that have be expropriated by China (more so true with Tibet) offer up a sticky determination of rights. China moved in tens of thousands of ethnic Chinese (Han?) to Tibet (not sure about Mongolia), so do those newer residents have the right to also determine the regions status. So yes, Mongolia should be unified, if the people desire it, without interference from the Chinese central government.
They are different branches of Mongolians, speaking very different languages. The writing are different now. Outer Mongolia has abandoned their traditional writing. That's why they end up with two different regions. If unified, they will compete for leadership. One is bigger but less population and less developed, one is smaller but more people and wealth. Even unified they will also distinguish themselves with each other.