Have you looked into the differences in the event dispatching models between IE and Firefox? How about the different ways to deal with URLS, or the different reactions to mixed SSL content across browsers.
You've obviously not developed a cross-browser application in HTML/Javascript... it requires the use of libraries to abstract away all of these differences, such as YUI, jQuery, prototype, dojo, or closure (plus MANY more). This creates multiple subsets of developers and methodology in the HTML/JS community, making it time-consuming to acclimate new developers as they join new teams. This makes it difficult to recruit developers in a scalable manner, unlike most other development platforms (including, but not limited to, Flash).
Don't get me wrong, I like HTML/JS, but it is significantly easier to develop *large* applications in Flash/Actionscript than HTML/JS. Smaller apps, single-page-scripts are better in HTML/JS, but unless you're using a sledgehammer like Google Closure or GWT, large Web App Development is still confined to Flash/AS.