Try understanding God's World View before you judge Him according to yours.
(I've oversimplified it, of course, because I don't really understand it either.)
This post responds to one I just discovered from a month ago by 
In a nutshell, the author's Five Reasons were:
- The Biblical creation account doesn't match science's current Theory of Everything.
- The Biblical doctrine of inherited Original Sin seems arbitrary and unfair.
- The Biblical hierarchy established by God is waaay too male centric.
- The Biblical God seems mean and has other negative human traits.
- The Vatican is not Biblical.
Here I suggest that all of this is because most people have a World View that is too limited to properly understand what God is up to and we are all too quick to blame God for the errors of men. Try on the following World View instead, and perhaps you will be able to see what a difference that could make on how you Judge your Creator. I have taken a few liberties with my metaphors for the sake of entertaining rhetoric. I assure you that the actual World View of the Bible is even more amazing. I'll leave cleaning up the differences between my lame metaphors and Biblical Truth as an exercise for the serious student.
Here I do not attempt to prove that the Bible is true.
I merely address the referenced accusation that
"God can't exist because He doesn't comply with our secular world views".
Submitted for your consideration.
- Christianity is not the Vatican.
- It is not the imaginations of the Renaissance artists who decided God must have a beard if he calls Himself the Ancient of Days.
- It is not the actions of bad people calling themselves Christians.
- It is not the actions of earnest Christians who screw up.
- Pointing to man-made religions claiming to be Christian does not make Christianity man-made.
Christianity is a World View that recognizes that no human can live up to God's high standards. It's members plead guilty of incompetent at meeting those standards and thus depend on the fact that God became a human, showed us how to live a perfect life, and died as a substitute rather than punish us for our failures.
God is long suffering and faithful despite humans thumbing their noses at Him at regular intervals since the beginning of time. He refers to Himself as our Father so that we can understand that he must discipline as well as nurture and love us.
There is more to this world than meets the eye. There is an unseen spiritual realm in which a war is raging that spills over into this one. On top of that, humans have free will and cause much of our own problems. God could intervene and stop all that, but at the expense of undoing His main objective:
To grow a "crop" of children who choose to serve Him instead of themselves.
To that end, he allows the weeds to grow with the crop until the end. It is the weeds that are the primary source of all the problems, but we all start out as weeds and are given the chance to change for as long as possible. If God wiped out all the weeds prematurely He would be cutting off every one of us before we had the chance to wise up. So He is thankfully patient with us and the result is the mess the world is in today.
But that is ok, because this temporary world is not the final end product.
This is like a "boot camp" where humans can gain the experience and wisdom necessary to decide whose side they want to be on. When boot camp is over, those who choose to be God's servant-children will be moved to a regenerated, un-cursed new world and everything starts over with a population of people who have chosen to serve there and who have demonstrated they can be trusted with much more responsibility. The rest, those who choose to reject God and elevate themselves to self rule, are discarded as unfit for service in His kingdom.
All this background doesn't mean God won't occasionally act severely (from the weed's point of view) to avoid damage to His intended crop. That crop will become God's family in the world to come, so He will do whatever it takes to protect those children from weeds who might choke the spiritual life out of them. Since He is the gardener, it is certainly His right to decide how long to tolerate the weeds and how much Roundup to use on them.
Our physical bodies are like expendable avatars in a video game. Our spirits are the end product being trained while animating those avatars. Physical suffering of the avatars generally makes for stronger spirits. Our avatars seem to us like all there is, and therefore seem much more important to us than God knows they are. He can and will reissue us replacement avatars in the new world - so all His actions are done with our spirits in mind, and appallingly (to us) little regard for our expendable flesh. Pointing accusingly to something bad that happened to someone's avatar is missing the point. Might as well complain to a video game developer that you don't like all the carnage that happens while you are playing. Questioning the morality of the Game designer only shows your own ignorance of the true nature of the situation.
Extending the video game metaphor, you can think of this world as God's Matrix or Star Trek holodeck. God can instantiate or modify anything at any time. Just like a video game or a holodeck program, he can construct the elements of the simulation in any order he pleases. If you read the Genesis account as the development log of a master programmer, it is not contradictory at all. Only if you insist that the simulation of Einsteinian spacetime has to be initialized at the beginning 13.8 billion years ago, and be run forward without interruption at 1 second per second, does your complaint that the Genesis account is out of order even make sense.
Since God is only interested in the final 7000 years of His spiritual bootcamp simulation, there is no reason why He needs to run the whole 13.8 billion years. When you start a virtual reality simulation do you have to wait for all the trees to grow from seedlings? Do you have to wait for all the structures to be built, and the materials mined? Do you have to wait 13.8 billion years before you can start playing the game? Of course not. The game creator bypasses all that and let's you jump into it at a set of initial conditions. In fact, you can pause the program and re-enter it at a later time with everything in the same state where you left off.
If we humans are able to build our toy simulations to do all that, why do you find it hard to believe that a universe Creator would do anything less?
If you find parts of the Bible that seem like they are over-simplified, it's because they have been over-simplified as much as necessary for humans of all generations and intellectual capacities to understand. That does't mean they are lies, they are just dumbed down to our level - and the level of the first bronze age people who needed to understand them. Even a caveman (or an atheist) can understand them.
I could go on, but those who have read this far already get my point:
Most criticisms in the genre that stimulated this post are based upon an entirely inadequate world model. Unless you have studied God's revelation far more than most, you are simply not qualified to critique Somebody who is able to create this universe. You don't know the requirements and specifications behind it and you don't know how to evaluate whether or not it suits it's Creators purposes.
You can only know what God chooses to reveal to you.
Study that, and it may be easier to put up with the way things are for a little while longer!