Come on now there is no shortage of qualified pilots to fly for legacy/ LCC airlines. Its only the regional's that have to worry. It's a gasp that they might actually have to pay a living wage for people to decide to invest their time in them.
I don't know if you would consider it a "shortage", but there are signs...FedEx and SWA have had guys no show for class. UAL/AA, at least, are getting called ahead of time that guys are not accepting their class dates. UAL, at least, is having guys leave during ground school to go somewhere better.
Then, why are they setting up Flow Through agreements, if they are not have any trouble flying their passengers. UAL just set up a flow through with Commutair, who they do not own.
The LCCs ARE having trouble. This is why JetBlue has flow through with Cape Air, and why they recently started Ab-Initio training.