The two biggest issues atheists have to deal with is that there is still no known logical way to account for the origin of the universe in purely naturalistic terms, and also the fact that there appears to be at least one thing in the world which is non-physical i.e. consciousness.
The two biggest issues theists have to deal with is the apparent evil in the world seems to make the idea of an omnibenevolent entity existing more improbable and also the supposed divine hiddenness of God which seems inconsistent with the notion of a personal God involved in world affairs.
Yes I know each side claims to have solved these issues. But there is really no actual consensus.
This is why the question as to whether or not God exists is still an unanswered philosophical problem. Both sides run into paradoxes when asserting their arguments. Humans will never know unless we die and go to an afterlife.