Before I begin, I'd just like to say that I am not against Flash. I have the plugin installed on both my computers, and I regularly and willfully visit sites with Flash content. However, I have recently noticed that there is a disturbing trend regarding the use of Flash. It is being used in ways it was not intended. It is being used in place of HTML because Flash is shinier. In my opinion, this is a bad thing. That said, here are some reasons why.
Because of the structured nature of HTML, it has been possible to develop user agents for people with disabilities, especially blindness. For example, a screen reader user agent may allow the user to listen first to all the headings (<hn> elements) on a page, rather than reading straight from top to bottom. It requires proper use of HTML elements and attributes, but it is relatively easy to write HTML that can be used effectively by a wide range of user agents. On the other hand, Flash is not structured, and does not offer such benefits. This is becoming more of a concern in recent versions of Flash, but it will be a long time before it will be on equal footing with HTML, which has had such concerns as a priority for many years. Furthermore, HTML is text-based, so it's easy for other programs to interpret. In Flash, text is just another vector graphic, which is not nearly as easy to work with. You can read more about accessibility at http://www.w3.org/WAI/
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There is a user agent which understands basic HTML available for virtually every computer platform in use today; most of them are free. What's more, the most popular platforms have user agents which understand very sophisticated HTML. Recently, an increasing number of mobile devices have user agents capable of displaying HTML. Though the Flash plugin is available for most of the most popular platforms, it doesn't begin to compare to the pervasiveness of HTML-capable user agents.
HTML Standards (http://www.w3.org/MarkUp/) are published by the World Wide Web Consortium. All the decisions are a collaborative effort of numerous computer experts from corporations and institutions all over the world. The W3C's mission is Leading the Web to its Full Potential. That is, they have what's best for the web in mind. Flash, on the other hand, is controlled solely by Macromedia. I have no faith in Macromedia to serve anyone's interests but their own2.
Leading the Web to its Full Potential
Due to it's text-based structured nature, machines can extract meaningful information from an HTML document. <meta> and <link> elements allow authors to convey what a document is about and how it relates to other available documents. This is a big part of what allows search engines to work as well as they do. Flash is largely image oriented, and as anyone who knows anything about computer vision can tell you, we have a long way to go before computers will be able to extract high level knowledge from images. Google can't direct you to a site where your keyword occurs in a Flash interface.
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It's not that you can't have links in Flash, but the system is internal. You can't really have the deep links that a collection of HTML pages allow. And of course, this whole linking thing is what makes the web go round. Link analysis is what makes Google such a good search engine. So, imagine if everyone make their sites with a Flash-only interface. Google's ranking system becomes a lot less useful. Also, this means that you can't bookmark things as easily. When a Flash interface starts, the address stays the same as far as the browser is concerned. After you wade through a flash site to find exactly what you wanted, if you bookmark it, that bookmark will just return you to the beginning of the Flash interface.
Just about the only way you can get lower is with plain text. However, it's definitely worth it for the added structure that HTML provides. Flash is actually a very efficient way to transmit vector graphics and animation. However, for standard user interfaces, HTML wins every time. Now, if you design a site with a lot of superfluous images, you can bloat it. Using JPEGs when you should use PNGs3 (and vice versa) will also louse things up.
Flash is a great multimedia extension to HTML. Eventually SVG may be even better. Either way, vector graphics are a fantastic tool, especially for animation. That said, they are not the best way to build user interfaces or deliver most content. As with any technology, people who misuse Flash only serve to tarnish it's reputation and impede its wider acceptance. It's just like anything else: use the right tool for the job.
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