Keeping flash without cloaking:
Things you can do to help without cloaking or changing your site to pure html. First off title tag your title tag should target your specific keyword or keywords try not to go for to many keywords. Title tags are very important and you should spend some time looking into the best possible title tag for your site. Remember not to make your title tag too big. The description tag is another very important tag this should contain a relative description to your page mentioning your desired keyword twice. Make sure not to over do your keyword relevancy if it looks spammy no one will click your link in the SERP'S(SEARCH ENGINE RESULT PAGES). If possible you can also include a title above your swf file using h1 or h2 tags. This way the search engines will at least get some relevant content. In the same way some company or product information in the body tag under the flash file can also help give the SE's(SEARCH ENGINES) relevant content.

HTML sites as well as flash:
I don’t like these kinds of sites and they really won’t work very well. Google mainly rank on IBL's(IN-BOUND LINKS) SO you have the choice of either sending all your links to the HTML version of your site and just ranking for the html version or link to your flash file and rank for both the flash and the HTML version. However neither pages would rank as highly as if your IBL's linked to the html site.

I’m my own opinion I would always change the site to pure HTML flash is an amazing application and in my own opinion should be used for web based applications. I would never make full flash websites they have poor SEO as well as poor accessibility.