What I find more interesting is that the people who usually love to hate on flash are the same people who break these rules when building poorly constructed "html5/css3/javascript" (buzzword overload) sites. There aren't a ton of them out there yet, but the number is growing. Nielsen's points are valid, but they aren't all flash-specific; I've seen these same principles violated in supposedly "standards-compliant" sites as well.

I think this bigger problem is a lack of true experience/interaction design knowledge. If you are only focusing on the visual aesthetic, and not spending time on thinking through the total experience, chances are you are going to make most of these same mistakes. The technology you choose is less of an issue, the real problem is how you employ that technology. That said, I always try to avoid flash unless it has a very specific benefit over css/js, thankfully I haven't needed to build something in flash in quite a long time.