Probably your two biggest challenges will be improving your GMAT score (which you already knew), and providig a convinvcing argument for why you want an MBA at tihs point in your career. Your profile is actually very similar to that of a friend of mine who failed to get into any of his target schools this past year (he also had a technical PhD and had about the same amount of work experience). I think his failure was in showing why now, after earning a PhD and doing so much work in a lab, he wanted to get into the business world.
Oh, a third point: You will also need to convince the adcomms that you will "fit in" at business school. Might sound a little silly, but remember that you will be surrounded by ex-bankers and consultants -- most of whom are in the 24-29 age range -- who have worked in the business world their whole careers. Your different perspective can be very valuable, but you will have to show that you "get" business concepts, and will be comfortable working with an all-business crowd. Taking some business classes before you apply may actually help on this front, but you want to show that you understand that business school is more than just accounting classes, etc., and that you're ready to immerse yourself in that world for two years.
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