I look at these club fees like I look at the cost of a dog. People ask: "How much is that dog?" Doesn't matter. You've got vet bills, food, kennel costs if you go out of town, etc. With soccer, you have the opportunity cost. It is so much higher than the cost of the cool backpack with the crest and the team name written in an elegant font.
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That is a great way to look at it. Who cares if the initial investment is different by a few hundred dollars. If you end up going to the same vet, buying the same food, using the same same kennels, the cost of the dog is the same. Claiming that one letter league is more expensive than the other is just another case of the pot calling the kettle black. If you are traveling outside of your county for league games, and have mandatory post/pre-season events, your soccer costs are likely the same as those participating in the other leagues.
Total Cost of Ownership is the real metric. I'd say generally speaking TCO for a higher level league within an eco system will be higher, eg ECNL > ECNL RL, GA >> DPL, NPL >> SoCal, etc. as there are usually more travel commitments for the highest level teams.
What's suspect is how some clubs play hide the ball where they don't tell you what TCO looks like for a season until after the contract is signed and the first payment has been made.