None is saying there is an absolute standards for excellence. For example,while Yale is widely recognized as a top Ivy school, it is also called one of the most overated schools. Except for its law school, how much else in Yale can you say is living up to its reputation?
What do you define as "serious stuff"? Only stuff such as nuclear chains and rocket science is "serious"? You have to understand higher education is more than one dimensional. Just hard science does not represent the full picture and spectrum of higher education. Even for computer science (one area in hard science), I am under impression that the fastest comupter in 1940's was from Penn.
OK, now let me inform you some fact about Penn, you can call me baised since I have stayed there for years before I moved on, but I am not going to disregard anything that's true, for example Columbia is certainly better known than Penn in China. Currently, Penn's medical school is #2 in the country, its hospital has been one of the top 10 in country for many years; its business school I guess I do not need to say much; its law school is also one of Top 10. How many schools have all thses schools in top 10? And according to online sources I came across, its annual spending is #1 among all universitise in the country (Yes, even Harvard included!). Although I have some difficulty in figuring out why they do and how they can do that with the relatively small endowment.
The bottom line, if you argue schools like MIT and Chicago are good, which is fine with me, then I think you need to stop keep pushing Yale to the front. Since at the fields you emphasized, there is really not much worth to be mentioned for Yale.