As SharePoint becomes more prevalent in the custom application development realm, there has been some friction and malcontent expressed in relation to deployment processes, team development methods and application upgrade paths. I believe that Microsoft has fallen short on providing the tools necessary to promote and support custom application development on the SharePoint platform.
In my opinion, the SharePoint platform should not limit nor impede my ability as a custom application developer to deliver solutions that follow the same deployment principals as any other custom asp.