People like to use images and animation to show off their web design talents, however these two things hurt your attempt to achieve a website that is search engine optimized. Search engines can only "read" text, they do not see the cute pictures and animations that you have on the site, and therefore they mean nothing to them. On the other hand, human users enjoy seeing these types of web design features. Therefore, you have to have established a happy middle when working out the web design features and the search engine optimization aspects.
The use of flash on the home page of your web design is ok, if you have text links that a search engine can use to navigate through your website. If flash animation is used as the home page and there are no regular links to follow, then the search engine is stopped before it even has a chance to index your website. The web design would incorporate the combination of flash with text links for navigation.
If you are concerned about the affects of using flash and other forms of non-textual web design, you a text browser such as Lynx to see how your site will look to a search engine, this is vital in the successful implementation of search engine optimization practices. If the site is hard to navigate, or you are not able to find all the pages within your site then you need to fix the links so that you can.
Above all else, when thinking about design and optimization techniques remember that content is king, bad or unrelated content will affect your traffic and search engine visits dramatically, search engines and human users are much the same, they both require quality content and relative information is you want them to keep coming back.