Yeah, Akihabara is cool, but gets overhyped a bit. Still definitely worth it. As far as the multi-floor arcade...um, could be several. I know there's a Sega Arcade that's several floors. Akihabara is really for the manga anime crowed more than it is for the videogame crowd. You can probably find any manga, anime, action figure, model kit, etc, you could ever want there.
Also, you should go to the red light district just for fun. Kind of fun to just see what all there is, although if you really want to you can go sit in a bar and pay 6000 yen an hour + pricey drinks to have Japanese girls dressed up in skimpy outfits flirt with you the entire time. I had some extra cash and really wanted to go to one simply to see what they were like, but the group I was with was 3 girls + me at the time, so that didn't really fly.
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Just that awesome
~InsaneOne