Even when they've done it right, like worked out the bugs and made it possible to navigate, there's still some issues that can't be rid of. For example, it is a law of the internet that every Flash based site absolutely must put all descriptive text in boxes that are hardly big enough for one paragraph (or one sentence from Robinson Crusoe, by the way I hate that book). This means that you have to scroll every other sentence. And if that's not annoying enough, you can't scroll with your scroll wheel because it's in Flash. So you have to hold down the scrolly-rectangle and drag it every few seconds. Then the low frame rate makes it choppy so you will lose your place. And if there's lots of text, you'll likely scroll past where you wanted to read since more text scrolls faster. If that's not bad enough, some sites like to animate the scrolling and give it ease, so it can't be too easy to scroll to where you want to. If you're on a product page, you can forget about learning of the product.
And don't forget that if you refresh, you're thrown back to the site's homepage. When the whole site is done in Flash, all the pages are in Flash. This can be fixed by separating different pages into different flash files and putting them on their own pages, but then you have to wait for the unnecessary animation and all that crap to load. Even on a fast connection, this will take longer than a simple HTML page.