I'm thinking, to make the site REALLY stand out, it would be nice to have a new method of navigation; the RPG style. so instead of the old boring menus (no offense), we would have a bird's eye view of landscapes and buildings.
Players would appear as little people in their position, and the stories would be found all around. You would get a map, and there would be puzzles that could lead to new areas and bonuses?
Also, this would make a points shop seem more real.
Duelling would be done at different sites, like in one area could be a RPS table, another could be a trivia board, a giant chess board on the ground... communication would be done with phone, so there would be a little option called 'phone' you could use.
Also, if we do go ahead with the trading card idea, this would be a nice setting for them (not too similar to pokemon though...)
The Forums could be a roman forum(s) with bulletin boards.
Articles could be a library
Games could be portals
'My Stuff' could be a base, akin to what is found in pokemon Ruby/Sapphire/Emerald.
except for the puzzle/bonus areas, the areas should be easy to navigate. various vehicles should be provided.
The proposed and long awaited member list could be a huge monument/statue with the rankings/hyperlinks engraved on the side.
Contests and/or massive duels could be held in a grand stadium similar to the Indigo Plateau.
Profiles would stay the same.