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According to the Patent, the Virtual Console bookmarks games via the characters featured in the games, or via the franchises related to them, and not boomarks games via their respective consoles, at least, not primarily.
The idea behind different character selection stems from Fig. 20, stating this:
FIG. 20(a) the second-game-machine game program comprises the game title, the game control program, the graphics data and the sound data utilized by the game control program as described above. In addition, as shown in FIG. 20, the graphics data included in the game program is constructed by the graphics data of the character of the hero or heroine in the game (the character graphics CG1 and etc.) and the map graphics data (map graphics MG1 and etc.). As described later, the data replacement program replaces the graphics data of the character graphics CG1 included in the game program 1, for example with the video data of the character graphics CGa for replacement. Therefore, the player can play the game character different from the original hero or heroine character as the hero or heroine. In the description of the embodiment, the explanation is made on the hero or heroine character by way of example, but the present invention is not limited thereto, and it is possible to suitably change the map or other characters.
This basically means Nintendo is allowed to rip the 'graphics data' (aka textures, models, worlds, etc), and manipulate or replace them without much hassle, and the replacements can be made at will via the Character Selection Screen shown
here. Its a rather ingenious idea, I mean, allowing you to chose games via their respective games franchises and characters.