Do you want to make the most of your site's search engine visibility? Do you want to rank for your bread and butter keywords? Do you also love your Flash introduction page? Well, you would be kidding yourself if you want to have the best of both worlds.
A SitePoint Forums thread asks if a Flash intro page can hurt your rankings. 99% of the time, it can. Your homepage is often the most linked to page on your site. Since that page is most likely to have the most number of links, it is your best chance at ranking for your most competitive keywords. If you do not put those keywords on that page, within the body content area, than you have a poor shot at ranking for those keywords.
Flash is much like having a picture on your site. Search engines have a tough time reading pictures or trusting the alternative text within those pictures. The same applies to Flash, search engines have a tough time reading them. It may be possible to utilize a Z-Layer of content under the Flash object, if and only if that content represents what is exactly in your Flash intro.
But all in all, you do not want to use a completed, 100%, Flash intro for your site. What you do want to do, if you love Flash, is to use Flash elements within your pages, like in place of pictures and so forth.
Forum discussion at SitePoint Forums.