Anecdotally, the professors I talked to in the building hated it. Non-rectilinear walls and oddly-shaped offices made it difficult to put up bookcases and desks. The windows were all custom, meaning if one broke, it was difficult to replace. And, of course, the aforementioned leaks.
I was in the Radio Society and had access to the Green Building (50) roof. The Stata Center actually looks coherent from that angle, and you can tell that was the angle the designers and approvers had been seeing it from (in model form) the whole time.
I saw the (a?) architectural model for Stata before it was built. I was with an artist, and we just walked into somewhere it had been set up for an event. (Yay for MIT culture of letting students go most places on campus.) It looked pretty crazy at the time. IIRC, there was a clear sphere embedded in the top of one of the lower roofs. My joke was that the model looked like someone had taken a paperweight, and smashed up a previously ordinary-looking building. It was crazy when construction started, and you could start to see elements of the building emerge, like, they are actually building that. (Though they left out the paperweight sphere.)
Before it was built, a designer friend, who'd worked worked in a Stata building before, mentioned the frequent complaints of Gehry buildings, such as people in triangular offices, or with slanting walls, that couldn't fit a desk.
Years later, I was surprised and deligted to end up working in Stata. My office was pretty generic rectangular and functional, with big windows that opened. No complaints about the office, except the HVAC couldn't win against the early GPU compute my officemate was doing. Space in the building was in demand by everyone, yet there were large areas of dead space. I wondered whether some of the conspicuously unused space was because they could've figured out how to adapt it, but was being banked consciously, so that space could be made for PIs who arrived later.
Stewart Brand criticized IM Pei's building for the original Media Lab (E15), as not being malleable like the "temporary" Building 20, and maybe some of the same criticism applied. Though Stata, coincidentally built partly on the site of Building 20 that was razed for it, did incorporate plywood elements in the interior, I think as a nod to Building 20. This included large plywood tables that were moved around as needed for different purposes in the open ares outside the elevator on my floor (G10?), multiple times a day.
The strange bathroom placement, and the ones that used visibly dirty ("green") water to flush, weren't a practical problem, but multiple times were awkward to explain to visitors. I liked the big single-person bathrooms on the office floors, and they were luxurious for students and professors doing all-nighters to get in a discreet paper towel bath, compared to the indignity of trying to do it in a toilet stall.
One thing I liked about the larger building design was the main street ground floor, adding cafe and various random seating, which was a big improvement over the Infinite Corridor.
At one point, I had a fair number of visits to a client's (IBM) IM Pei-designed facility in Somers (NY). There were so many oddly-shaped conference rooms in the pyramidal buildings.
He was pretty open about his design process, and I think he did voice this: https://www.youtube.com/watch?v=ENa2Hmh3lGU
The building replaced a beloved Ww2 era temporary structure that lasted 50 Years.
Making a statement with architecture rarely goes well, especially if you abandon rectilinear structures.
https://www.rle.mit.edu/media/undercurrents/Vol9_2_Spring97....
I toured at MIT when I was applying to colleges, and the student narrating the walking tour trash-talked the Stata Center pretty brutally as we went by it, mentioning the leaks, the lawsuit, how nobody liked it, etc.
I never knew if those were her actual feelings or if this was part of a script approved by the admissions office, or even which of those possibilities would be crazier.