The Afghanistan 2009 Presidential election recently attracted a lot of media attention due to its blatant fraudulence. It was supposed to be conducted using plurality with additional top-two-runoff round if necessary. In fact, there was massive, blatant, obvious fraud evident to all external observers and widely reported in the press both before, during, and after the election. [We shall not give details since they have by now been widely reported elsewhere.]
H.Karzai declared himself victorious with over 50% "hence" with no need for a runoff. However, under pressure from international observer groups and consequently the USA, he later reconsidered and agreed to allow a runoff, i.e. essentially, admitting his fraud. It seemed likely Karzai would have won even with honest voting, and it also seemed likely that in the runoff he would just re-fraud the election anyhow (this time more subtly). His rival A.Abdullah therefore dropped out of the runoff, claiming it was pointless for him to participate since he saw no way to prevent such fraud.
Some voting systems are more susceptible to fraud (and when that fraud occurs anyway, it is more obvious and easier to detect); some are less.
Before the war the literacy rate was estimated at 11.4 percent (18.7% male + 2.8% female). In urban settings 25.9% (35.5% male + 14.8% female) of the population six years old and over were literate, but in rural areas only 8.8% (15.7% male + 0.6% female, in some provinces 0.1%).Unfortunately the 2-round system is bad because it is two rounds (a severe imposition in a poor country like Afghanistan) and also, that clearly failed in the present case since Karzai initally refused, and then Abdullah refused, to permit the second round. Just using the first round alone (i.e. plain-plurality voting) would also have been unnacceptable since it delivers results which, when there are 41 candidates, are almost random and hugely undemocratic.
Both asset, and plurality voting (as in the top-2-runoff system) and especially approval voting permit enhancement via Rivest-Smith antifraud technology, which although it would probably be too complicated for contemporary Afghanistan, could be a useful idea to hold in reserve for the future.
Afghanistan has a lot of problems which may prevent it from becoming a successful democracy anytime soon. But bad choices of voting system would severely-hurt that goal.