At least the $99 fee keeps hordes of amateurs from uploading their 'hello world' app and clogging up the review process even more.
But yes I see your point about overloading the review process.
Developers aren't "paying nothing" to develop on IOS. Apple has factored in that the average free app costs them $99 per year in hosting costs.
I am certain 98% of that $99 goes to compensate for the top 10 free paid app's costs to Apple.
Related: Quite some time ago [Edit: OMG it was 10 years ago!] I had a game on the App Store that I stopped updating and pulled because the $99 fee wasn't covered by the low number of downloads. Many people were still playing the game at the time, but I just couldn't justify the cost.
And WHY should Apple even review and approve apps that run on hardware YOU own!! When you buy a fridge, does the manufacturer review and approve your groceries?
No, the FDA does that. Apple needs to approve apps because there is no FDA equivalent for apps.
Apple is a self-serving private company, not beholden to user's interests (but shareholders), with an extremely fluid, arbitrary set of "laws" (if you can even call them that).