LWJGL:
* no multiple windows
* no multiple Canvases
* no multihead head support
If you want to build a 3D level editor which mixes OpenGL perspectives and regular GUI widgets JOGL is the choice.
I appologize if I am completely wrong, as I most often am; but... If you look at the demo's for JME (mojomonkeycoding.com) you will see just this. 4 canvases and gui widgets. From what I've seen, it looks like all the rendering is done using LWJGL. I'm just beginning to look through it so I could be off base here. However, from what I've seen it does look possible to create these features.
I've been in a similar pattern for the past 3 months. I've been trying to absorb as much as I can out of what is out there. My 3D skills are on the newbish side and I haven't been developing in Java for too long either. I've looked at Xith, LWJGL, JOGL and various java game engines.
I noticed a lack of documentation for LWJGL right off the bat. I kept searching over the website thinking that I was missing something. Then I noticed in the faq that someone else had been trying to figure out the same thing; there isn't any. On the otherhand, it seems straightforward enough that you "could" pick it up from the java doc.
From reading forums, I get the impression that there are some things missing in jogl. I also get the impression that even though jogl has the backing of Sun, it still doesn't have that many active developers. I'm also curious to see what happens now that Sun has necro'd java3d. I haven't found a whole lot of "jogl" documentation and code, but I have found some. Enough that you can couple it with the extensive amount of opengl documentation out there and really start to piece it together. It's strongest attribute is it's "standardness". Although I've read of senarios where the tricks of regular opengl programming require alternate tweeking in the jogl world. That makes it slightly more challenging then porting some c++ code and thinking you've got some really slick optimized classes.
As I mentioned eariler, currently I've been looking at jME. There are a lot of little test programs that are easy to follow and the design is rather intuitive. I've found it to be a good learning tool, which for me was the most important.
My personal view is that there isn't an API out there that takes the cake. I believe that java has a long life in the gaming world. Rightnow it is rather immature and very rapidly developing. Bottom line is, go with whatever you find easiest to learn; in another year we might all be using that new microsoft api that is supposed to replace directx. The way things are going, who knows.