The discomfort of the stick isn't so bad that it can't be ignored, or grown accustomed to, but it pales to a genuinely comfortable controller. Two hours into Perfect Dark while sniping hard sims in the Villa, the stick will whisper, "Hey! I still suck!" Or while executing consecutive Mario Kart power slides with a string of bananas strung out on the Z button, the stick with slide out from under a sweaty thumb in defiance. BOO-URNS.
They're easy to replace, but the aftermarket ones are worse. The replacement sticks are on larger, heavily-weighted ball joints that make them more durable, but less accurate for fine control in the center area. On the outer extreme, they quickly conform to the hard, 8-way mechanical guidance that limits true 3D movement.
As for Doom, the default controls are pretty bad, but easy to customize. Just put strafe on the R or Z button.
