Imagine if some teams only played 15 times in that time. Others play 24 or more.
Imagine if some games when for 2 quarters rather than 4. And some 6.
Scores, percentages, ladders, wouldn't really create a true representation. Finals would be wrong - with teams playing more games and more quarters being advantaged.
The NPL is faced with the above scenario in trying to work out who should get a ticket to the finals.
No system is correct! No system is accurate. Finals in anything are the result of who was the best over an even amount of events and conditions (all things being equal).
There's so much luck involved. There were some venues where 2 or even 3 of the top 5 were also in the top 50. All of a sudden the 7th and 8th placed people are given a ticket, yet someone finishing 6th somewhere else, where no one was in the top 50, misses out.
As I said earlier - if it wasn't a smart business decision to make the change after season 1, then it wouldn't have changed for any real logical reason (I would assume).
Averages in anything... either have no restrictions, or a "minimum". Test cricketers can't be considered in the top 10 batsmen until they've played 25 tests. If it was capped at 50, then Steve Waugh, Sunny Gavaskar, etc.. would have monster averages over those who play 25 - 50 test.
As Pete wrote, reward the players who play lots (without forgetting they are playing lots because they want to, regardless! And playing NPL is a reward
In the end though, the actual final itself should work it all out