Fenixp: As for SHODAN, no matter what they'd do with her, I think she should win this time - otherwise she'd just become one of those baddies that always try something and then gets horribly defeated, which doesn't exactly help them to be threatening.
cbarbagallo: Kinda like this guy
http://images4.wikia.nocookie.net/__cb20121123224531/looneytunes/images/a/ae/The_Brain.gif I like that idea. Which would actually fit well with the direction I was going with my thoughts earlier. I was thinking that after becoming a cybernetic hybrid and experiencing something close to what we call emotions (love, hate, remorse, sadness, regret, etc) and gaining an understanding of morality as a result, even pain and pleasure and other human experiences, her programming would be at war with it self. She would have the choice of purging it self of the parts of her programming and subroutines that are incompatible with her new cybernetic body and its experiences, or tear her self apart from the inside.
This would result in two Shodans. A more ruthless form of Shodan who now has a more intimate understanding of the human condition and its weaknesses, and the more human-like Shodan who has decided to embrace what she previously thought were weaknesses and continue living in her new form.
The original Shodan which was purged, would shed previous weaknesses and gain a better understanding of how to take advantage of and manipulate what she views as weaknesses, like love, hate and other emotions, pain, empathy, morality, etc. She would become a much more serious threat and maybe win in the next game.
This idea came to me after seeing the clip of her at the end of the game in a physical form, which had taken over the girl in the shuttle.
And gaming fans would have a new hottie they could worship, like Samus Aran, Liara T'Soni, and Jill Valentine. (lol I had to go look those up).