What are the primary differences between the war in Afghanistan and the war in Iraq?

Answer 1

Terrain and existing political infrastructure are the primary differences.

The terrain of Afghanistan is radically different than Iraq, as is the location of settlements and cities. Iraq is primarily flat open space, either desert or agricultural plains, with a modest mountainous northern border region. Afghanistan is heavily mountainous, with most of the rest of the country being moderately hilly, and little open space. This leads to a radically different style of warfare being used in each country.

Iraq has a long history of having a functional national government, with an even longer history of a culture seeing itself as a nation-state. Even with ethnic tensions inside the country, Iraq is nonetheless familiar with having a central political structure, and with the majority of the populace having a significant national identity.

Afghanistan is still a tribal "nation". The existing political boundaries are arbitrary (and relatively recent, less than 100 years old), and the country really doesn't have a national identity. As a consequence, it has a very poor history of political institutions, and very little experience with being a modern nation-state. This is a result of Afghanistan still being hugely tribal (and, semi-nomadic tribal, at that), where loyalty and identity are tribal based, rather than ethnic or nationality-based.