From what I understand, a common downfall when it comes to proving genocide is the specific intent requirement. According to the Convention on the Prevention and Punishment of the Crime of Genocide, acts like killing, raping, forcibly transferring, etc., must be completed with the specific intent "to destroy, in whole or in part, a national, ethnical, racial or religious group."
While the int'l legal community in general might quickly agree that this intent was absolutely present in Sudan, international courts and other governing bodies seem to be less inclined to easily conclude the same. It appears they are more likely to conclude that yes, horrible attrocities happened, and yes, this person may have deliberately "inflict[ed] on the group conditions of life calculated to bring about its physical destruction in whole or in part...", but we aren't quite satisfied that those actions were done WITH the INTENT to destroy the group in whole or in part. And you simply must have both: the actions and the intent. It's a general principle of criminal law. SO, here, maybe the actions were taken because the group is hated, or because Bashir doesn't care about human life, or maybe he even knew that taking such actions might very well lead to the destruction of the groups, but all of that still may not show that he had the specific intent when he carried out the actions. For the record, this is not my opinion. Just some thoughts on the issue.