bodad is correct. Look at the distribution of the two.
The major populations of Shia are found in Iran, part of Iraq, Yemen, Lebanon and part of Afganistan.

Sunnis are widespread, from eastern Europe and Turkey, Africa, Saudi and the Emirates, central Asia from Kazakstan to Pakistan and Bangledesh and east to Indonesia and southern Burma. There is a very wide range of religious practice. The Pushtun tribe of western and northern Pakistan and adjacent Afganistan is very restrictive; the Taliban are the younger generation, educated in the madrassas only on the Koran and a few other Muslim texts, and are struggling to regain power in Afganistan; attempts to eliminate them are ridiculous.
In Pakistan, authorities are careful to leave local power in the hands of the locals in the more traditional Pushtun areas.

Afganistan has never been a viable country; the central area and Kabul being Shia and the rest Sunni. Rulers holding power in Kabul never conquered the Sunni, esp. the Pushtun, regions of the country except for very short periods. Cooperation, not forced compliance, kept the area peaceful for long periods, and unified in the struggle against foreigners.

Iraq is the result of the forced break-up of the Ottoman Empire following their defeat by the Allies in WW1. The Ottomans never were able to force rigid controls over the whole area. Break-up of Iraq into areas depending on culture and tradition, Shia, Sunni and Kurdish, is probably the best solution, but opposition of Turkey to Kurdish independence, and how to split the income from resources such as oil are deterents.
Bagdad, unfortunately, is close to a boundary between Sunni and Shia, hence developed a mixed population, even mixed neighborhoods; controlled under Saddam Hussein, but now descending into sectarian chaos due to the interference by Bush.