There is still Unity 3D as a decent 3D competitor.
Flash still has many other limitations besides 3D. And its not like java was winning awards at every corner for awesome 3d web games.
I personally think 3D for web based games will always be limited for many years, due to the very nature of 3D games tending to be much larger file size wise. Also significantly more complex for programmers with more advanced math and other problems.
I still personally have very very high hopes for JavaFX 2.0
One of the biggest things I think that is undertapped/utilized is the fact that you can have a in browser applet, then drag/drop it onto the desktop, for it to be played offline(or non browser) later. You can also generate windows/applications free floating outside of browser, in all java forms I believe. Whereas flash and unity are currently stuck in their windows?