I started with the JavaScript API originally. I had no problem with it, well documented and easy to learn. Mostly just worked in Notepad++ and Firebug. A little later when the Flex API came out everyone started asking for it, so I started using that. Again I thought it was pretty easy to learn. It wasn't until the iPad came out that I had to go back to JavaScript. No one was trying to use a huge viewer on their phone, but the table makes it more practical.
At the moment I split 50/50 between JavaScript and Flex. I have no problem going back and forth, and I will say the Viewer for Flex makes rapid application development a breeze. I am also less worried about cross testing in different browsers (but differences do come up from time to time). That being said when a client gives me the choice I use the JavaScript API, it's just the way the industry is going and the skills you develop will help if you ever want to work with more JavaScript libraries (jQuery, Dojo, Leaflet, Google, Openlayer, etc).