The question is not "should I change from Java3D to something else ?" but "Can we mix Java3D and JOGL ?"
If it helps, consider it is a very old project for a company who doesn't want to spend time and money to change the underlying engine
So I know we can easily mix JOGL and Ardor3D / Xith3D / JME / WorldWind Java / JReality / etc.
And because the approach is different in Java3D, the abstraction is stronger between Java3D and JOGL,DirectX or OpenGL, I'm asking if we can do the same ?
It appears that nobody seems to have done this here, too bad
Concerning the health of Java3D, it is not a problem because I already use a modified version, maintained by myself.
Concerning Xith3D, I don't think it is very active these days.
It is not because a lib is not growing anymore that everybody should drop it, Java3D is very stable and does what it claims to do, which is what I look for
Take a look to this project, it shows that Java3D can perfectly fit some needs event today : http://www.sweethome3d.com/index.jsp
And I'm not saying that Java3D is the best engine, just that it is stable enough to still be used today, just like other engines mentionned before.