It'll be a long time (if ever) that WebGL catches on due to Microsofts conflict of interest with OpenGL. So looks like Flash could do really well in this area.
Microsoft will never adopt WebGL except if this technology has a huge success. However, WebGL has no chance to succeed without a proper MSIE support.
As for Java, Oracle have done some nice changes for the client side stuff but sadly its not enough and unlikely to be anytime soon. They've wasted alot their clientside resources into JavaFX which has been a rather big disappointment and caused them to neglect core Java.
Giving up JOGL is not what I would call a nice change.
Don't think Java is either reliable or particularly quick for web based 3D tbh. Certainly not well adopted or supported.
Half decent flash 3D will be far more widely used, even if probably a lot more limited.
Jake 2 works reliably as far as I now.