I have not played the Steam version, but the DS version contains a cleaned-up translation (particularly in the tech names), better menus, and beautiful, detailed minimaps. The extra dungeons are nothing to write home about. Personally, the thing I like most about the DS version is that my battle commands are on the bottom screen, allowing the top screen to just be devoted to the graphics and animations. The DS version is unfortunately harder to hack, but I consider it the definitive version.
I've heard good things about the Steam version post-update. The launch was a catastrophic failure, but it sounds like the team actually fixed it up.