If the GPU is not the bottleneck but the CPU is, then its not really JOGLs fault, is it? I mean, if you cant keep the GPU busy enough (by comparison) that means you shouldnt worry about JOGL performance?
I would have said the opposite!
If the CPU is the bottleneck, then the problem lies with JOGL and Java (and specifically JNI otherheads).
Conversely, if the GPU is the bottleneck, then Java cannot be the bottleneck.
Though to be fair, the issue here is a poorly designed app. not the speed of Java or JOGL.