The problem with your analysis is you are comparing apples to oranges. It is a meaningless comparison. If the extra pax generate extra revenue and at the same time increase incremental costs then it makes no sense. That is why you need to look at fuel/ANM.
At the risk of stating the obvious, that's just another way of saying that both seat-km and aircraft-km costs have to be factored into fleet planning decisions.
So, for example, the 747 will have a lower cost per ASK than the 737, but if you're only getting 737-sized loads ...
And since competing manufacturers don't make identical aircraft, any comparison is never going to be 100% apples-for-apples.