Replacement of Flash?
With Silverlight not picking up, and Flash not supported by Apple, most Enterprises want to know the 'universally acceptable and compelling' technology to use for building Flash style presentations. HTML5 with XML could be a fit. Are there any other emerging technologies?
It would be important to keep an eye on Unity3d.com - the company has healthy relationships with hardware device manufactures and their respective SDK teams. They are built into the google chrome browser on desktop, and have integrated many monetization features across multiple screens.
HTML5 and CSS with a little Java... but if you are looking for software to help build all this, I have been using Adobe MUSE for a while now and love how easy it is to create almost anything you could want, including linking to animated elements and embedding them.
HTML5 and CSS3 are widely accepted and load quickly on desktop and mobile devices... don't forget the mobile users - don't lose them due to heavy load times. Keep it super lightweight these days. Think of the end user always. What do THEY need in order for you to make the hook/sale? Do they really need a fancy animation? Often the answer is no unless it's an entertainment/gaming site/application. Users are more often than not looking for information in order to make a purchase either now or down the line.
Enjoy the day.
HTML5, Jquery is the way to go. I been using the Reveal Framework for my online presentations, a demo is available here - http://lab.hakim.se/reveal-js/#/
You can fork it from here - https://github.com/hakimel/reveal.js
HTML5 has native support for Canvas, there are other technologies like SVG etc.
Infact, recently developers have even built beautiful effects using simple div elements. (HTML)
Look at a demo here: helloracer.com/webgl/
From what I read below, your chief concern seems to be a great UX without losing the SEO benefits. If that is so, I would suggest you take a hybrid approach of combining Flash, HTML5 & CSS3. What you could is to break up and reorder your website's content into SEO centric (where you primarily use HTML5) and UX centric (where you use Flash). Further, no harm in repeating content which you need for both.
HTML 5 is the best way to go. Open Source.. is much better a standard than propriety players like flash.
HTML5 along with CSS3 animations work well. I've just built a site using these techniques at www.tommaddocks.com. The site is responsive, and animations work on smartphones, tablets, etc.