#1. Orochimaru is NOT dead. Just making that clear.
#2. Wind fights akatsuki b/c akatsuki kidnapps kazekage.
rice fights akatsuki b/c orochimaru used to be part of it, but since he left, they are now enemies (oro and aka)
fire fights akatsuki b/c akatsuki killed sarutobi asuma, (hey, these are spoilers, but if you arent up do date, you shouldn't be in this thread at all) and they attempt to kidnap naruto. at this point, naruto+kakashi+the other guy (the mokuton user, i forget his name) killed one guy, shikamaru permanently trapped another, and sakura+the old lady from sand killed the puppet guy (sorry, i just woke up and can't remember any names)
the only one that doesn't make sense is water fighting aka, and water doesn't fight oro either, so that wouldn't be any more unrealistic than it already is
#3. We might as well leave oro be...changing it would be a pain for neji, and it wouldn't really make the game better...
also, then we would all be like "oh, now <insert next "boss" here> got killed by <insert naruto character here> so we should change it again!"
on that matter, who sez sasuke is evil at all? he just wants more power. he doesn't (that we can tell) kill anybody, and when he fights that massive army of ninja, he leaves them all alive. all he wants is to kill his brother, but up to now he hasn't done anything "evil" (yes, he beat naruto, but didn't kill him, which is the important thing.)