4meg of apache dependancies? log4j is only 352k and ant is purely optional (and only if you are building). We could abstract the logging a bit so a light weight logging .jar could be substituded in at deploy time (I wouldn't be surprised if someone has already created a light weight version of log4j with the same method signatures already which would save us the effort, I am only speculating though).
Dealing with native libraries is a pain.
1. (prefrably) deploy with java web start, this removes most of the pain
2. at runtime (i.e. in your shell scripts) specify the java.library.path (-Djava.library.path) to point to your .dll directory
For developing (probably not recommended for deploying as you may run into version problems if your user upgrades although it would technically work).
1. copy the .dll's to the current java.library.path (query the System class to find this out. The Xith3D install guide
has some good info on doing this. It's basically the same as odejava - just different .jar files.
Regarding Xj3D - will you be writing a custom display package for Odejava? It currently supports Xith3D and Java3d. It's quite simple to add new display packages and there are already some docs on doing this. I'm happy to answer any questions you may have.