Given that the accused is currently in control of the crime scene, it's not surprising that the prosecution chose to prioritise the crimes that are easiest to prove.
The ICC does not state only 41 deaths ocurred. GP is pulling that number from an unrelated Wikipedia article that is undergoing an edit war. It went from "63k" to "41+". None of the commentors here justifying the low number realize its completely made up and unrelated to the ICC