Hi there,
I did an Osaka-Kobe vacation recently and here's my small review of it! I was living in Tokyo last year and my girlfriend at the time and I decided to go somewhere not too far away that had many things to do, and settled on the same area it appears you're going to.
Universal studios is a theme park. It would be fun as a diversion, to see how the Japanese do a theme park vs. the West, to experience the rides and attractions, etc. But, at the end of it all, you're at a theme park. So, that means line-ups (some excruciatingly long), high priced food, etc. Don't kid yourself, there's nothing special about the USJ experience aside from the fact that you're surrounded by Japanese people and all the shows like Waterworld and even ET speak Japanese. It's one of those things that was cool to do as a diversion FROM Japan when I was living there, as opposed to something I'd wanna spend limited time doing while visiting Japan, if that makes any sense.
Kobe on the other hand.. I can show you some of my photos.. it's a nice place. Since the earthquake they've obviously had to rebuild a great deal in a short amount of time so it's a very 'western' looking place. It really resembles the waterfront area here in Toronto and probably other major cities. Modern architecture, shops, lots of diversions, etc. That being said, it doesnt disappoint (in my humble opinion). There's a great buffet restaurant, regularly scheduled boatcruises around the port area, lots of interesting shops and things between the main station (Sannomiya I think its called) and the port area. If you've got the time, a short taxi ride will even take you to their earthquake memorial museum which is a great place to learn about and reflect on the tragic earthquake of 1995 which killed 6,000 people.
Personally I can see the merit in doing both but you may walk away from USJ going 'well why the heck did we go there, we could have done that in the States'. I cannot honestly says USJ is a must-see above and beyond anything else. But even if Kobe isn't blow-your-socks-off exciting, its still more authentic and visually stimulating in my opinion.
some teasers:
Buffet restaurant in this building (photo from April 2007, it should still be there!)