"Maturing up" a video game, eh? Well, when doing that I think there are three things to keep in mind:
1) There is nothing wrong with adding to a story. That is how stories are made: diffrent people contributing ideas and puting them together. Video game plots are no diffrent.
2) Since the original story is known to a younger age group, that age group must know that this story is not for them. Also, everyone must know that this is not the auther's original story or a offical exstention of.
3) Maturing a story opens a lot of doors (Agh, I sound like a parent!). Make sure you are using them to further your story, rather than maturing for maturing's sake (i.e. having the charictors run aroud half-naked for no other reson than "It look's sexy").
As long as those three guidelines are kept, I think that adding mature content to a story is a good way to increse the story's level of depth.
Hope I could help!