Having a story line center around two characters isn't bad, but it's kinda hard to do it. They mustn't feel the same, you really want to make them feel different to play. But the step from one character to the next shouldn't be that different that it makes it hard to control and switch between characters.
But that aside, yes Motoko lives in too different a world.
Also as I'm doing a computer siences studies and I am willing to help with this project.
Also what I seem to see a lot these days in games is that they want so many gadgets and gimmicks that you spend the first half of the game being introduced by it, just look at GTA 4, you're easily 2 hours into the game and the last thing just got explained to you, if you like sandbox you could have already spend 5 hours on the game. So be carefull with what you want in the game and what not.
Further what I like about most RPG's is that you need to learn how to use something first, I'm going to fetch another game for this example, take the FPS RPG Bioshock. I enjoyed the game and all, but there was hardly any RPG in it, you could use any gun, plasmid and hack anything. The only things that was a bit RPG-ish was the tonics (if I remember the name well), but on easy mode you got enough of them to boost everything up (don't remember what it was like on hard). So make sure it is an RPG.
What I personally think is a good RPG, is great story line (and telling) and 'real' RPG elements. Learn how to use a weapon, magic (magic schools? (both as in places of learning and as types of magic, such a conjuration/summoning, necromancy, divination, etc)).
Ow and I'd download a game featuring Mana (as soon as I have money I'd buy it
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