Pros:
Creating a Flex mobile project is easier (use Flex 4.6 with design mode to rapidly prototype, 4.7 to develop) and visually let's you drag and drop
You can use data binding and other convieniant built in tools
Like anything else, there's good and bad about using the Flex mobile project as oppose to a complete ActionScript based solution. Mainly, it's a lot easier to customize your preloadeder, your splash screen and other features similar to tht like customizing how your application handles screen. Below is a couple pros and cons of using the Flex mobile version instead of ActionScript.
Cons:
Slower performance
Can't use Adobe Scout, it's an awesome tool for real time benchmarking and profiling. Using the built in one is ok but it doesn't give you theamazing information that Scout provides.
My advice: if you're savvy enough to do everything in ActionScript, then definitely create an ActionScript project, your users will love you for it. Plus, it's not that much harder and it lets you have a myriad of additional control over your components. Also, you don't have to deal with the overhead that comes with data binding ( it generates event listeners, get and set methods and you can create much more efficient ones on your own). There are a number of other things that benefit you by creating an ActionScript version like refactoring and better subversion but those are more of incentives than anything else.