OK, I'll take a try at this.
There is a lot of truth in what is said in the article, if you read it very carefully.
The final solution is not a military one; you start with the military securing the country (making it safe to bring in others) and then you have to bring in the NPO's (Non-Profit Organizations) to take care of, and educate the people. Challenges here include: culture and mind set. As a people, the Afghans are not as educated as the Iraqis and it may take longer to educate them to a level of understanding.
You also have to build up the country's ability to defend itself by itself and this may take more time (than Iraq). One example of why, is a briefing I heard where soldiers were teaching mathmatics to the Afghan men so they could properly use artillary (they didn't understand our math). If you can't properly use indirect fire, you only have a short range fighting capability.
Another factor is culture. Many (rural) Afghans are mainly concerned about their tribal unit and not the one in the next valley which is over the mountain.
There are other issues too, such as (re)building infrastructure, and the logistics is a huge matter when you look at the geographical layout. (But this is just a quick comment.)
