Share 'disadvantages of customizing code?'

I understand that when you start customizing your code you no longer get automated upgrades...so what is the process of upgrading like for those of you that have chosen to customize? A lot of my interest in using Ning is driven by the pain and suffering caused by five years of customization on the drupal.org CMS. I love the idea of not being responsible for security any longer or for the periodi…