This article seems to point at the real issue: http://www.mystatesman.com/news/news/uber-threatens-to-leave...

Basically, that allowing cities to specify the implementation and rules around fingerprinting makes the onboarding process too slow. Slow enough that that they can't hire drivers fast enough to meet demand.

I can see their point on this, since each city is free to make their own rules for the process.

On the other hand, if they volunteered their own process...one that incorporated fingerprints and most of what cities are asking for, then perhaps there's a place to meet in the middle. Basically, a single process that works for all cities.

As it stands, it looks like neither side is willing to compromise.