Hello, I am a current part-time student in the MS&E program. I would say your GPA isn't a problem, since I got in with a lower GPA than yours. I would think that things like GPA and GRE scores are negative filters, and GPA above 3.5 should be good enough that your application is automatically filtered off without being reviewed by the ad com. Definitely retake your GRE though. If your GPA is below their average, I guess a GRE above their average will look better on your application.
It's not a MBA, so I think diversity of the class is not a key criteria, though I do see a significant portion of the class being international students. Work experience is also a plus, since quite a good % of the class has some working experience despite it not being a MBA. If you manage to get your GRE scores to a nice level, you will need to focus to draft a great SOP and secure good letter of recommendations to stand a good chance of being accepted.
Good luck!