The current version of Universe does not do system generation. HE is a system generator.
On the other hand ...
- Universe allows you to keep lots of notes and hides referee notes from players.
- Universe creates pretty maps.
- Universe can import and export in a variety of formats (and even lets you create your own formats).
- Universe allows SQL searches of the data.
- when editting a system Universe is rules aware (including all the original Alien modules).
Also development on HE has been abandoned whereas Universe 2 is finally due before end 2009. (A major part of Universe 2 will be system generation.)