The game itself isn't flawed. There have been many proposals to deal with overtime in order to avoid the crapshoot.
The fundamental problem is twofold: First, because soccer is played worldwide, there needs to be consensus among the over 200 participating nations in order to make any changes. Think the United Nations to the fifth power. Things move along at glacial rates. Second, the governing body, FIFA, is corrupt to the core. So nobody trusts them to do the right thing, making it even more difficult to reach any consensus.
In 1995, a new rule was added that prohibited the keeper from using his hands when the ball was played back to him by a field player. People were clamoring for this rule for over a decade before it was implemented. The inertia is simply staggering.
Frankly, I'm surprised the refs have been allowed to use the spray to mark off the 10 yards on free kicks. This has been standard practice in South America for some time, but I just assumed FIFA wouldn't allow it for this world cup.