If you aren't already aware of it, check on http://www.vmware.com/support/developer/vc-sdk/visdk400pubs/ReferenceGuide/ then click on Data Object Types and search for VirtualMachineConfigSpec for all the options you have that you can change there. For that matter, if you do a search for VirtualMachineCloneSpec, you'll probably find a lot of other cool options for cloning. That link is probably the second most important tool a developer can have right after his computer.
EDIT: I just noticed you said Java. Same stuff applies, it'll probably just be something like configSpec.setNumCPUs(2);