I used the SAP project module for about 6 months in 2012. I found it to be quite cumbersome and not user friendly. That could have been the way my employer set it up or because the training was given in half Spanish and half English. Outside of the delivery method or set up, the interface was simply cumbersome. Compared to MS Project 2013/2013, SAP is not as valuable as a PM tool, in my opinion, as MS Project. There are tools out there that are a bit more robust that MS Project but Project is the most common tool out there. Especially with 2013 being retooled, I am quite happy with it.
SAP is an ERP solution for the entire business processes such as administration, budgeting, accounting, purchasing, management, etc. It originally was written to control investments and the cash flow for projects.
MS Project is focused around project planning, scheduling, control and monitoring. It is more of physical monitoring of project rather than financial monitoring. There is element of cost monitoring in MS Project but it is still not in detailed format and exhaustive as SAP. At the same time SAP is not as user friendly and too many steps to complete a simple process. Whereas MS Project is lot more simple and easy to operate. Most of the project manager and engineer working on site find it easy to manage project using MS Project.
There is another tool coming up in the market called TIEMCHART. Its founder is having an experience in SAP and build the platform that takes the advantage of both SAP & MS Project into one nice web based platform. Try them out if you are looking for an alternate solution http://tiemchart.com/