I don't recall the article ever saying they invented anything new, they just put all the pieces together (i.e. designed it) such that they expect a 50-70% drop in fuel consumption.
Since the designs and their problems are well known, they have quite a lot to work with to figure out how to make it all work.
It's like the B-1 Bomber - such wing designs had been around for years, and the potential gains were well known. The trouble was, until the B-1 was developed some people thought the inherent instability in such a design was insurmountable, and such a plane would never fly (because all other attempts always crashed).
But then, someone figured out how to compensate, and now it works great.
MIT is well known for their engineering and technology programs, they are about as prestigious as a tech school gets. Given the number of technological innovations that come out of MIT, it's quite likely this is yet another MIT breakthrough. They can be pretty sure by running it through their simulations, but won't know for certain until a prototype is actually built some years down the road.