Having just redone my own website, I might be able to help. From what I understand and what I experienced myself, it goes like this.
The main disadvantages of flash are this:
1. It doesn't display on some devices, notably the iPad and iPhone, and doesn't display well on most mobile phones.
3. It is not good for SEO as bing and google cannot see inside of the flash content. That means all text information in your website cannot easily be indexed by the search engines. If your business relies on people finding you on google or bing, a flash-based website will not work for you.
The main advantages of flash are this:
1. It looks the same on any browser and works with legacy browsers. With html/java your website might display differently depending on which browser people use, and look horrible on some old browsers. Sure, you can code it in such a way that it works almost universally, but it is a huge pain in you behind (at least it was in mine) unless you go with fairly simple design and menu elements.
2. Image scaling works, and the scaled images look great. I could not get it to work as properly with a html website, but that might have been due to my lack of coding skills.
After struggling with this for a long time, I decided on a hybrid approach. My main website is flash based, but has an html version for search engines and flash-hostile devices. There is also a separate ipad version. An attached blog helps with the SEO. Since most of my business doesn't come from search engines this works for me. It might not work for you if search engine ranking is what you are after. I tested a few companies when I looked for a new design and in general, it seems to be the case that the initial loading time is longer than a html site, but once the site is loaded navigation is quick (and depends mainly on the size of your image files).
I hope this helps. Let me know if you have any more questions.