Talking about fans there is surely a differentiation between Milan and Inter for the same stadium. In FIFA 12, indeed, if you play home with Milan you get home fans in the blue area, if you play home with Inter you get home fans in the green area. So that's absolutely right. On derbys the situation is simply a merge of the two, so positions are still given in a good way.
On the other hand, maybe the space given to away fans when Milan/Inter are home, is too much, but I don't think you can do something for this because that away fans space is vital for the game when there is derby.
The rest of the stadium is almost neutral and that's the error... but sincerely, given that orange and red area are inverted in the game, I don't know how to deal with it. Without editing the wrong structure, maybe you can simply convert neutral fans in non-press area, in some more colourful home fans, with few flags (like they are now), with no banners (like they are now), but with some scarvs, if possible!
For the rest, if you want to see some coreographies, just look at this video and the related ones:
http://www.youtube.com/watch?v=rS6ZDAY4jLw&feature=related
The question is: if Milan home area becomes away_team area when Inter plays, is there a way to differentiate these two situations? Why am I asking this? Because if there is no chance, then it is quite odd adding lots of banners and flags that would add lot of unneccessary atmosphere to away fans... In this case the only chance is making TWO versions of the stadium
What do you think Sido? Did you get what I mean?