I am most familiar with Windows, so I will speak from that perspective.
Because software was an application, and the path of least resistance was to use the OS provided controls and menus, there was a sense of uniformity in how you accessed features. Keyboard shortcuts just worked and were pretty much the save (Ctrl-S, saved the document, etc).
OLE provided a uniform way to embed documents into other applications. Cut and paste worked consistently.
There were also a limited amount of frameworks (bare Win32, MFC, OWL, Visual Basic, and Delphi probably covered 95%+ of apps).
It seemed that most user interfaces at the time were actually made by programmers and not graphic designers. In addition, for the most part there was a lot of continuity from version to version in how a program looked.
Now it seems that every web app wants to look different for the sake of looking different. People want to change how an app looks on a regular basis, often for no other reason than that it needs to look "fresh.". There are a myriad of every changing front-end JS frameworks.
It seems that UI is driven by graphic designers looking to make something unique and standout and not programmers that just want to make a standard, low friction way the user can access the functionality and be done with it.
Also, all you data is siloed a lot more because it is stored in the "cloud". Whereas before you could easily have access to the raw output from all your programs (and if they supported OLE embed documents from one program in a completely different one), now it is somewhat of a pain if you want to get raw access to your data.
Web based apps do have a lot of advantages, but I feel we have given up a lot when we went from native desktops apps to web based.