Well, since most of what I do is client only, I may not have a good answer, but hopefully others can tell me whether I'm thinking correctly or not. I believe you can use java webstart to run a normal app, and by that I mean a JFrame based app as opposed to an applet. I think users would rather run your game through java webstart than in a browser.
If you are using frames, you can just have your classes call other frames, which can accept input. This input could be fed into a data managing class. Before I would even start on this game, I would practice on implementing some guis first. You don't sound like you have a lot of experience so I wouldn't recommend developing a game as your first ui option. Then, after you have some experience, i would spend some time with your friend and talk about the design of your program before you ever write a line of code. This will keep you much more organized. Good luck. I'm sure you'll have more questions, so keep them coming.