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What are you looking to get out of the program? For the most part they lead to different outcomes.
The MBA will broaden your career opportunities in a way that the MEM can’t. Also, zero people looking at your resume in X years will know or care that 50% of your courses were with Yale SOM, and to most, an MBA is really not about the course load.
Do you want to learn the textbook skills to manage environmentally-focused businesses? MEM sounds great. Do you want to build a network of international business leaders and open doors outside of clean tech (e.g. consulting, banking with the intent of returning after building your business fundamentals)? Do an MBA.
This bowl is obviously MBA-centric, so I would say do the MBA. In my mind, it’s almost always better to get the broader degree and focus your efforts rather than get a super focused degree. MBAs can still get jobs in clean tech, probably just as easily as MEMs.