This whole Flash "war" makes me laugh. You know, the war between Apple and Adobe's Flash product.
Flash was introduced as a lightweight version of Shockwave to display basic animations on a webpage in a time when online video didn't exist. Flash became ubiquitous today not because of its video abilities or ability to run ActionScript/Flex, but because there was a real need to have high-quality animations and dynamic elements on an otherwise text-and-pictures web. It was a quick install (and Microsoft included it with IE, starting with IE4) - and it instantly made web pages more attractive, which was a breath of fresh air during the early web.
Flash's popular use as a video player only came about because Adobe slipped in video capability right in the middle of a time when Apple, MS, and Real were all vying for the easy-to-use browser plugin market. Suddenly someone realized that everyone had Flash player, which suddenly introduced video support, then Youtube came out, and then virtually overnight Flash became "the way" to play video online.
Flash's popular use as a web app platform (cartoons, games, etc.) also came about at a time when the "interactive web" was really taking off and web devs quickly realized that to get a Java app up and running that looked good and worked well was next to impossible - and to try to do the same thing with just HTML and JavaScript was even harder given browser incompatibilities - not to mention you pretty much were giving away your source code if you decided to do so. In fact, by this logic there are plenty of websites out there that are nothing more than image galleries that are still done in Flash because the web dev feels that the site will look better in Flash vs. just doing it in HTML.
So we have three main uses for Flash:
1. Embedded ads, animations and hover buttons
2. Embedded video
3. Fully "Interactive" web sites or applications that look good in most browsers.
It is pretty obvious based on this list why Apple couldn't care less about Flash. If it were just about animations they would have licensed SWF from Adobe and implemented it natively in Safari in the same manner that they implemented animated GIFs. However, it's not. It's about implementing all three or none of them.
Flash for embedded video purposes is really only a stopgap because MS, Apple, and Real never really agreed on anything, and HTML5 seems just as good for this purpose, especially since IE9 will natively support HTML5 video. Mozilla will figure out a way to play H.264 in Firefox, trust me on this one. My guess is that for websites that just need embedded video, it will eventually no longer make sense to choose Flash if it means your video will play everywhere, even on mobile devices.
Interactive websites, well, this is where Apple is drawing a line, evening know ing that they are blacklisting a very broad category of websites (from say, a mortgage calculator to a complex 3D game) - but they know that Flash on a mobile device will more than likely feel "lousy" on a phone to the point of frustration. Heck, sometimes Flash apps are lousy on a PC, too. Apple wants everyone walking away from the iPhone saying, "wow, that was really fun and easy to use" - not complaining how the text was too small or that scrolling around some 1024x768 Flash app was annoying. They know that users are more offended by empty promises then no promises (yes! our device supports Flash... well sort of, except large apps, or hovering, or video camera support, etc...) Apple is one of few companies left today that admit that the web may be the future, but sometimes the web browser just isn't the right place for some applications. They would rather see more basic web apps, or have you write a device-specific app, (which, I think, you can compile and submit to the App Store using the latest version of Flash.) From a developer's standpoint, it is harder, more annoying, and more expensive to write a native application for any platform, but Apple knows that for a large majority of the cases the native app from the user's perspective will be more enjoyable to use over the same app made in Flash, Java, or HTML+AJAX. This is a pretty large gamble on Apple's part, because while this is true, this just means that fewer apps will be available for their platform, even if they are crappy.
Just a few hover buttons, etc. are rarely done with Flash anymore (they used be done in Java, remember that!) these days, so this is no longer a concern. With regards to advertising, I suppose Apple is just making a judgement call that no one will miss embedded animated advertising on their mobile devices.
The biggest sufferers here are the web sites that are "accidentally" 100% Flash, e.g. Subaru.com's "build your own" page
(here). Attractive sites like this are still hard to build using HTML+JS, but wouldn't make sense to make an app out of, either. I don't even think HTML5 makes building "subaru.com" any easier, either. Perhaps some new "Dreamweaver of the future" will come along that will make creating awesome, animated, standards-compliant HTML5 websites possible with the click of a mouse, but I doubt it will be from Adobe. I expect this gap to last for awhile, but even at that I don't think it presents any major issues. Sites like subaru.com are an exception to most websites, and will almost definitely stay that way for awhile. So we'll see sites being developed for more than one platform (nothing new here), or sometimes websites just won't work on Apple hardware (nothing new here either). In both cases, companies follow the money and do what they need to do to get their content across, so I'm not worried about usability - it really hasn't affected my usage of the iPhone in a very negative way.
Adobe could have worked with Apple to make a custom Flash player that better supported the iPhone display or multi-touch, met battery level standards, etc., but my guess is that it never happened because Adobe didn't want to make the investment or bow to Apple's bidding. Adobe wants to make Flash a universal platform, so they're going to invest more in creating a Flash player that is more suited to various devices but on their terms. Personally speaking, I think this is a mistake given Sun attempted this with J2ME, and going head-to-head will only further fragment the existing market while Apple slowly, unaffected, builds an ecosystem of native apps. Whether this is better or worse for the common good, I do not know. For the foreseeable future, I think plain HTML is still the only safe bet for content that "works" on all devices.
When the iPhone came out the big selling point was that it was "the whole web" so there is no reason to believe that Apple wouldn't at least contemplate providing support for a significant fraction of the web's content. This is hardly a "war", it is really just two companies going in different directions.