SharePoint Custom Application Development Methodologies

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.net application. As some readers may be aware, at present the standard Microsoft guidance is flawed because it does not fully support repeatable build processes. This is a huge barrier for custom application developers who are accustom to building applications using source control for all assets, build automation and continuous integration. SharePoint as a lot to offer but taking advantage of the platform as a vehicle for custom applications show be more congruent with standard software development practices.