First of all, I'm not stating I'm making one or planning on making one, I'm simply stating a few ideas for such.
P42 and I came up with several ideas, many of which I don't remember, being it was a while ago.(try and remind me, Prower).
Now, to fit some of the theme of the Anime, I think the game should be an Action MMO, like Atrix Online. Also, there's a special way you create a navi at the beginning of the game;
First, you make the basic outfit of the Operator and Navi
Next, you create the PET
Then, you set the default weapon of your Navi (if not selected, would be the classic buster.)
Then, you roll stats
Lastly, you create the emblem of your navi, which makes you unique
In terms of net exploration, I think It should be virtual representations of actual websites rendered by the game.
The viruses in the game would either appear at random, like the classic RPG style, or you can find real viruses and eliminate them.
Which leads me to my next point, this game should also double as an anti-virus tool. That way, you could stop real net criminals, and delete viruses from your PC at the same time!
If any of you have any other ideas, feel free to post.