What is the difference between fontSize and textScaleFactor in Flutter?

The default for fontSize is 14.0. Therefore, textScaleFactor: 2.0 appears to be the same as fontSize: 28.0 as seen in my code example:

class MyApp extends StatelessWidget {

  @override
  Widget build(BuildContext context) {
    return new MaterialApp(
      home: Scaffold(
        appBar: AppBar(title: Text('Title')),
        body: Row(
          children: <Widget>[
            new Text("Jane", textScaleFactor: 2.0),
            new Text(" Doe", style: new TextStyle(fontSize: 28.0)),
          ],
        )
      )
    );
  }
}

What are the pros and cons? Are there any recommendations when to use one or another in specific cases?

There's no difference between them in the rendering. What changes are their purpose.

Font-size is usually a per-component value. While the scale factor is more global. The fact that you can override the scale factor directly on the Text is just a bonus.

In your typical application, you'll have the following:

MediaQuery(
  data: MediaQuery.of(context).copyWith(textScaleFactor: 2.0),
  child: Whatever(
    child: Text("Foo", style: Theme.of(context).textTheme.headline),
  ),
);

Basically, consider textScaleFactor as a zoom option. While font-size is used to separate a title from its content.