I agree with what Nepalean has already mentioned before. MS is more research oriented and hence you need to be creative and come up with research ideas. ME is more project oriented. One other thing that I would like to mention is that getting admission in MS is harder than getting admission in ME. So some people just enroll in ME and then after a semester or two switch to MS upon the approval of the department and a good GPA. But the result is basically the same besides the fact that MS also opens the door for PhD. Usually professional experience is preferred than a class project and so I don't think it makes much difference whether or not you had a project unless it's outstanding and you can prove that to the employers. So in my personal opinion MS is better than ME.