As with most objects on the internet created with Flash (or similar third party software), creating a navigation with Flash will cause problems for some users and search engines. Search Engines struggle to index anything that is not HTML or XHTML (whether this is strict or transitional), SERPs cannot follow links within flash or any other third party script. In addition to this you are limiting your audience by forcing them to use Flash Player**, regardless of if this is previously installed or not it will take more time to load the HTML or XHTML.
(X) HTML and CSS
*Flash and Flash Player refer to Adobe Flash and Adobe Flash Player.