We often get asked by customers ... why did you decide to design your interface the way you did. Good question! In prior times when we were developing on Lotus Notes we tended to make improvements to the interface where we saw fit. It seemed to make so much sense - we'd make it look way better for our application area, which was as it is today - collaborative work and project management. Once we started developing on the SharePoint platform we stopped this practice!
Many customers are being introduced to the SharePoint interface (like it or hate it!) so it does not make sense to add a different interface for project management on SharePoint - as it actually frustrates users and slows deployment. We figure when you deviate from the standard SharePoint interface and architecture then even simple user tasks like using datasheets and even something as simple as finding a report becomes difficult because you are not using the SharePoint Quick Launch. Similarly simple customization tasks like adding columns and creating useful views are all made unnecessarily difficult. We built pmPoint starting with standard SharePoint lists, web parts, sites and site collections. As such pmPoint uses the standard SharePoint interface where available and any additions are added right into the SharePoint interface where we figured the SharePoint team might have added them! It has make adoption way smoother over the years. Now with SharePoint 2010 our customers have to get used to the new SharePoint interface and we will move with it - keep life simpler and thus more efficient for everyone.
So in answer to the question - "SharePoint User Interface - Keep it or Change it?" ... Keep it!