Harvard and MIT have a lot of clout, and it's partly because of how incredibly massive they are. The Harvard network has more professors than some universities have pupils, (above two-thousand). Consequently just the amount of output due to a large number of people working there gets it placed high up in rating indices and such.

It's tough to say if it can keep up with its reputation. In some ways this phenomenon is comparable to gentrification: the beauty and soul of a place sometimes dies when the people who made that place what it is are displaced, like how Somerville and Berlin changed/are changing. It makes no sense for someone to remain committed in an academic career track when they're paying the kind of rent they do when around MIT/Harvard area with the income they make, so I agree with you that it's no longer attracting the kind of people that made MIT what it once was.

There are some institutions, that not many know about yet, that I'm confident in a couple of decades everyone will know about like U of Copenhagen and KIT & U of Stuttgart in Germany, and I think some in the midwest (Purdue, UMich, etc.) will one day have their day to shine too.