Well, there is one obvious way to cut through all these strange rules. One entry per country, period. Each country sends its national champion to the big tournament of champions.
But...the thinking of the ISU is swayed by the objection that the second best skater in Japan is probably better than the national champion of Indonesia, so various rules are put in place to allow extra slots. This would be a valid point if the ISU World Championships were a contest of individuals.
However, the ISU is not an association of figure skaters, it is an association of national figure skating federations. Each federation has (in principle) equal status with all the others. Why should Japan get to send three skaters and Indonesia only one?
As an extra bonus, the "one country, one skater" idea would elevate the prestige of the national championships.

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