I absolutely love D3, it's what we've been seeking for a very long time and finally a decent product was created. Prepare to see this blow up and take over the web soon.
The problem with flash is the same problem as the .Net framework, Coldfusion and similar technologies.
You cannot have an entire ecosystem revolve around a single company and not have growth or compatibility problems. You simply can't.
What flourishes? Things like Linux, Python, etc because they can be flexible and adaptable. When you have a company in charge of a technology you will always be at the whim of that company and what they decide to do with it.