For example, you could be working at Google / Facebook earning top $$$$ every year and you paperwork could be spotless. But the stress of having to go through an uncertain renewal process every 3 years prevents you from investing in big things like buying a house or having kids. You are always worried about being able to return back to your stuff when you leave for a trip overseas.
Even though most top companies immediately apply for Green CArds, the "country of birth" based green limits ensure that you have to remain in H1-B status for 15 - 20 years (if you happen to be born in India).
TL;DR: It's not the increased vetting that we fear, its the uncertainty and complicated appeal procedures that can affect genuine H1-B cases.