This first one I noticed immediately upon starting with Win 95: The clock on the bottom right corner of the screen can be formatted for all sorts of international standards, but none of them display the seconds. In Win 3.1, it was very easy to display the seconds, but none of the versions since then have had it.
The second one took me a long time to notice, and I suspect that’s because it went away very slowly. First from one application, then another, until nowadays it seems to be totally gone. Back in the Win 3.1 days, if you would press the F1 button, or click an on-screen Help button, the software knew what screen you were at, and often even which field you were at. The result was that your request for Help would often yield some useful info about what you were trying to do. But nowadays, I almost always end up at the home page of the software manufacturer’s website, and I have to go through a whole tree of options and/or type several paragraphs trying to explain myself. Aaargh!
Other stuff too, but I wanted to get the ball rolling with these.