If you're asking about what the best poker league system is then the answer is simple: It doesn't exist

because it depends on what you're after. A ranking system should promote that which you think is important. Attendance? Then give everyone who attends points. Aggressive play? Make it top heavy. Nitty play? Top light. Want people to feel they have a chance even though they missed the first tourneys? Only grant points for the X best tourneys (as you've done). Etc...
To illustrate this in another way:
If you want to be 100% accurate in how the players are ranked, then there is really only one way: Net profit. However you look at it, a player who has netted (after deducting buyins, re-buys etc) $80 has done better than someone who has netted $75, because poker is valued in money! Any other points are artificial, because it rewards things that have no value. For example, getting points for bubbling is purely artificial, because bubbling has the same value as busting the first hand: 0. But I think almost everyone would agree that using net profit as a ranking system would absolutely suck for many reasons. So the "best" system from one point of view is the worst from other point of views.
One of my pet peaves is when every spot is worth more than the previous, like place 12 gets you more than place 13. Why? Because you lasted longer? Maybe you didn't? Maybe you busted in 12th after 15 hands, but the player who busted in 13th place played 16 hands on another table? So why are you getting more points??
If I ran a ranking system, I would probably award everyone 1 point (reward attendance), slowly progress one or two spots before the bubble (add some artificial value to the bubblers), then ITM progress the points roughly in relation to the payouts (to mimic the actual value of those spot).