An HTML application, while it has to be more carefully written to work in all browsers, has the benefit of working on many more platforms. Flash isn't always stable on Mac or Linux, and it only exists on a few mobile platforms. It's not even supported by iPhone (and never will be) or Android (will be in 2.2). Not to mention that while Flash will (probably) be less used in the future, whereas the new features of HTML and JavaScript will keep becoming more prominent on the web.
So my suggestion is to go for a HTML solution if you feel up for it. If you're not very experienced with rich web apps, but you have worked a lot of Flex, maybe you should go with Flex.
Basically it boils down into how much time you want to spend on the project. I think you will get the best quality in the end if you choose HTML/JavaScript.