The current World Cup format of a group stage followed by a single elimination tournament lacks in many respects. The most important is that there is a very important luck element due to "soft" matches or "soft" teams which make their appearance during the final round of the group stage. Some teams have to play their last group match against very motivated opponents and other teams play against "soft" opponents that have been eliminated or have already progressed. This is very unfair. Also, there is always the possibility that teams facing each other can both progress with a certain result and that result tends to happen. This has happened many times in the past.
A solution to this is to start using the double elimination format. For the ones who don't know, it's a format where the first loss puts a team into the "loser's side" of the tournament (to continue the tournament playing against other teams that have also lost one match) and the second loss sends the team home. This way there are no soft matches and soft teams, as a loss has grave consequences (while still leaving room for recovery). This system also guarantees at least two matches per team. It also guarantees that there is no need to schedule matches to start at the same time and it guarantees that a team cannot drop points on purpose to face an easier opponent.
In the double elimination format the final is played betwen the winner of the "winner's side" (that is, an undeafeated team) and the winner of the "loser's side" (that is, a team with one loss). On some double elimination tournaments the team coming from the loser's side has to win the other team twice to win the tournament. On other double elimination tournaments a single final match is used, which means that the winner of the tournament can have the same number of losses as the runner up.
Whichever final configuration is used is still better than the current system, in which a team can have losses or wins against soft sides and still win the tournament against a team which reached the final undefeated.
Also, in the double elimination tournament there are only two matches guaranteed per team, while the current system has three. But the only way to play just two matches in the double elimination format is to lose your first two matches, which almost always eliminates you in the current format as well. Think about it, in the current format a team that starts with two losses has zero (e.g. Bosnia) or little (Honduras) hope to progress anyway, and most likely they are looking forward to the plane home instead of to play in the pitch.