Flash pages don't help in getting higher rankings on the search engines. Even though search engine algorithm has been improved over the years, they still find it difficult to index flash pages. Search engines clearly note that they index text based elements & hence flash pages are at a disadvantage. They should not be used for navigation & home page text. Noscript was used in earlier times, but its excessive use lead to spamming & hence search engines discourage their use now.
Whenever flash is used, an alternative HTML should be made available. Many websites provide both a flash version & HTML version of the sites. Top level navigation should be in text as it helps search engines follow the links & index the properly. Also sites should be included in Google & Bing webmaster tools to know how search engine bots are treating the pages. Content is still the king & providing fresh & updated content to the search engines help improve the rankings of the pages.