Keep it flat

Jar files are Zip files with another extension and a special (and optional) folder named META-INF. For each file or folder there is a header associated. As headers take some space of the jar you better keep less files in it, but if you already took it to the bare minimum then keep all those files in the root directory.

For MIDlet distribution the jar file must have the META-INF folder so, for best space usage, your jar files should have only this folder. Your MIDlet and all other classes should be on default package. The same with resource files, keep all of them at file root.