I don't see why it's even an issue various point systems are flawed in different ways. Some encourage offense while others reward defense. They all have their own merits and flaws. No system is perfect and satisfies everyone. After decades of debate and numerous playoff models, even big money college football hasn't come up with a perfect system to determine national champions. Can you expect a perfect point system for youth soccer tournaments? At the end of the day, if your team wins outright, you advance. Plus, tournament point system has very little bearing on your kids' long term development.
A perfect system would measure just game results, with a win worth a certain amount, a tie half that amount for both teams, and a loss worth nothing (2-1-0 or 6-3-0). That pure system allows calculation of a WLT percentage that is fair among a large number of teams and a large number of games, even if not all teams play the same number of games. However, in a short series of games such as happens in a weekend tournament, there would be a lot of ties in the standings and thus the need for a lot of tie-breaker rules.
The 6-3-0 10-point system (bonus point for goals up to 3 per game, bonus point for shutout) has been fairly common over the last few years in soccer tournaments, derived from the NASL scoring system that first appeared North America in the 60s. NASL included the bonus points for goals scored up to 3, but not the bonus point for a shutout. A bonus point added for shutout wins (and sometimes for shutout ties), and points deducted for red cards, is the most common system seen around here in youth soccer tournaments. This sytem has the advantage for tournament organizers in that it rolls most of the tiebreakers into the standings points. One complication of that system is what to do about forfeit wins - should they be scored as 1-0? 3-0? award the shutout point or not? A forfeit win could earn anything from 6 to 10 points.
The ancient 2-1-0 system has pretty much disappeared from soccer tournaments, replaced by the 3-1-0 system in imitation of the 3-point win rule first seen in English professional leagues in the early 80s. That bonus point for a win is fair if all teams play the same number of games, but requires some clumsy adaptations when not, such as the average-points-per-game used in Cal South State Cup when selecting wild card teams across groups who have played different numbers of games. The 3-point win supposedly encouraged more aggressive offense and thus more scoring, which is usually meaningless in a 2- or 3-day youth tournament. I have also seen a hybrid system something like the classic 10-point system, except that a tie is only worth 2 points, thus preserving the ratio between wins and ties as in the three-point-win rule.
No matter what the system, there will still be need of tiebreaker rules, for which there are so many variations that it would be worth its own thread.
An interesting website with history of scoring systems --
http://homepages.sover.net/~spectrum/scoring-systems.html