As I look at the export for the project I noticed that the project archive (zip) file includes a lot of JS libraries that my project may not be using. Thankfully the project index files do not include the unused libraries. However I did notice that the project is using un-minified versions of the jQuery libraries. You could start there.
Also make sure your image files are small and compressed but not to the point of losing resolution or quality.
Use the Developer Tools (in Chrome) to discover the lag times in your page loads.
Check to make sure that any browser extensions are not performing unnecessary background processing.
Just a few things I do to cure a sluggish browser app. I'm not surprised that the Flash version is faster and more responsive. But it would be unfair to compare a Flash app to an HTML/CSS/JS browser app. It's like comparing a movie to a stage play (not the content - just the method of delivery).
I hope it helps.