I certainly think that one particular and marked difference between both thinkers is how they view the institution of government. Montesquieu took a rather modern view of government. The idea of divided government, separation of powers, is one where government is large enough to need segmentation. Montesequieu's view of this government is representative, in that individuals elect or choose people to occupy these branches. In the end, there is a political compact agreed upon: Citizens elect officials who occupy these branches and act accordingly. Montesquieu's vision of government is one in which citizens' interaction with their government is more clinical and detached. They elect, officials act, and the process of voting is where affirmation or negation exist.
Such a modern view of government is contrasted with the Classical notion of government's interaction with the people that Rousseau seems to indicate. The General Will is a compact in which individuals actively partake in their own government. The government is an extension of the citizens' own wishes and desire. Rousseau argued that the community's expression of political freedom is the definitive element to indicate freedom. In this, Rousseau seems to be suggesting that government cannot function without a complete submersion of individuals and their governing bodies. It is to a point where citizens' interaction with government helps to define their own sense of freedom. This is intensely different from where Montesequieu sees the issue of government's interaction with its citizens.