Ron Rosenbaum thinks Catch-22 is the latter:
People speak too narrowly when they talk of Catch-22 as a satire of humanity. It's that, yes, and there are few better. But it's really a vicious satiric attack on God, as much as his poorly made creatures. This denunciation of God comes from the heart—Yossarian's, anyway—and transcends any denunciation of the evil of war. It's about the evil of existence itself and the creator of that existence and that evil.
He holds up this rant of Yossarian's as proof:
Good God, how much reverence can you have for a Supreme Being who finds it necessary to include such phenomena as phlegm and tooth decay in His divine system of creation? What in the world was running through that warped, evil, scatological mind of His when He robbed old people of the power to control their bowel movements? Why in the world did he ever create pain? … Oh, He was really being charitable to us when He gave us pain! [to warn us of danger] Why couldn't He have used a doorbell instead to notify us, or one of His celestial choirs? Or a system of blue-and-red neon tubes right in the middle of each person's forehead. Any jukebox manufacturer worth his salt could have done that. Why couldn't He? … What a colossal, immortal blunderer! When you consider the opportunity and power He had to really do a job, and then look at the stupid, ugly little mess He made of it instead, His sheer incompetence is almost staggering. …
Earlier coverage of Catch-22's enduring legacy here.
The Dish 