That would be much harder to fly under the radar because fingerprinting is what you do to people who are arrested. People wouldn't put up with that so easily.
There's been some rumblings of the "uniqueness" of fingerprints being far less than you'd think. Fingerprinting everyone who flies would just produce more false positives. The people that's bad for overlap a lot with the people who stand to benefit from invasive security theater.
I'd be very interested in any source material you have detailing these 'rumblings', both from the first hand experience of having been fingerprinted (which is oddly misrepresented in TV and movies) and from a general interest in forensic history.
As a child I recall an antique book on criminology which spoke glowingly of the reliability of fingerprints in investigations, and cited the unsuccessful defense of one convict who claimed (sometime in the late 19th century) that fingerprinting was a 'hazy and fallacious method imported from France, where many innocent men have been convicted by it." It is true that juries have an unfortunate tendency to believe in the first order results of any technical procedure, from ducking stools to DNA matching.
Some guy from IIRC Texas got arrested in connection with some letter bomb terrorist stuff. IIRC the only connection was the fingerprint. His lawyers basically assumed he did it until some other law enforcement agency finger printed some guy in North Aftrica who fit all the other evidence (i.e. he was known to them as the kind of guy who would be involved in that stuff) and his prints matched as well. I saw it mentioned as a small anecdote in a paper/article/blog about the "rigor" of the forensic "sciences".
There's been some rumblings of the "uniqueness" of fingerprints being far less than you'd think. Fingerprinting everyone who flies would just produce more false positives. The people that's bad for overlap a lot with the people who stand to benefit from invasive security theater.