The good thing about the middle seat in PE on a 787 is that you can alternate which neighbor you "disturb" to get to the aisle. That said, it's an overnight flight, are you really going to be getting up a lot? You might want to advise your neighbors in advance, maybe one of them would switch to the middle.
Also, keep in mind that the major drawback of an economy middle seat (squished shoulders) doesn't really exist because of the wider seat and the wider armrests. So it really shouldn't be that bad.