The one-time fee is an e-stamp, basically. It makes having N identities N times as expensive as having one. It's one of the oldest anti-spam suggestions, from before spam filters were invented.
What you're talking about with that "license" is exactly what you get by everybody relying on a small set of KYC providers; except that the KYC provider doesn't charge you for registration, but instead requires a Proof-of-Stake in some state's legal system (i.e. a set of documents that require laborious up-front proofs to acquire, such that it's very hard to acquire two sets of them, but which can be used to validate identity freely once issued.)
KYC providers that just charge $100 instead of requiring a Proof-of-Stake challenge exist, too. That's essentially the (secondary?) purpose of businesses that will only trade with other incorporated businesses (or, to abstract that away, only with businesses that have a Dun & Bradstreet DUNS number): it costs $100 to incorporate, or to register one of those numbers, so you have to be at least $100 of serious to bother them, and you can't just keep spending hundred-dollar-bills forever to keep generating new identities to DDoS someone.
What I haven't heard of, interestingly, is a KYC provider that requires a proof of work. Something like "solve a thousand Captchas to create an account." Or a formalized version of the old "take a photo of yourself holding up today's newspaper." But that'd be totally workable as well.