I agree, when Tom and Kaya have dominated events this season and yet aren't in the top spot, it does seem like the AFP ranking system is out of balance, even if they have not participated in as many events as other athletes.
On the other hand, Tom has done well enough this season that if he had just shown up to one other slope event this season, he would be in first place, as only the 5 best results count.   Since I don't think Tom is done with his competition season, given his amazing year, I imagine he'll still take the top spot in slope whenever he competes in a fifth event--probably either at Euro X or the AFP Championships.
That said, I think there is a larger problem.
I don't think Gus is the best skier in the world.  Not even close.  My reasoning is that in spite of competing in 20 events this season, he has only been on one podium at a Gold or Platinum event -- a first place finish at the North Face Open in Whistler -- which means that there are about 10 athletes in various disciplines that consistently beat Gus whenever they choose to show up.
The reason I think this is a problem is that the AFP's legitimacy is contingent on their ability to select the best skier in the world.  If that selection doesn't represent who has had the best overall season in a significant percentage of our minds, it isn't a legitimate award or organization no matter how many points and formulas they use to calculate it.
I think there are three problems within the AFP system that lead to this problem
1.  They count too many results (10) toward the Overall Ranking.  I think an athlete should be able to win the major events, win the overall and film a great video part in the same season.  I don't think the system should reward the athlete that shows up at the most events.
2.   AFP should get rid of their limits on specific disciplines counting toward the Overall rank  (4 SS + 4 HP + 2 BA).  The system already benefits athletes participating in multiple disciplines.  An athlete only needs to finish in 5th in three X Games events to have more points than another athlete who wins slope at X Games and two Dew Tour slope events.  There is no need to double penalize an athlete that dominates in one discipline.
3.  There is too much reward for just showing up at the X Games.  There should be a greater fall-off in points between different ranks at all levels (Platinum, Gold, Silver, Bronze).  Case in point, if you finish 9th place at an event at the X Games, it's worth more points than winning a Dew Tour Event.   Since they had essentially the same field, this seems out of balance.
I think if the AFP wants to be taken seriously and has any hope of elevating our sport to the mainstream, it needs a legitimate ranking system that accurately reflects the general consensus of the freeskiing community.  As of now, AFP has failed to do so in my eyes.