I am not entirely in agreement with you, as the apps that were launched from the Apple menu from 1984 up until System 7 were actually special apps that were allowed to run on top of the main app, back before the Apple could multitask. This is a holdover from the pre-hard drive days, when applications were not actually installed but lived on their own 3.5" disks. With System 7, Mac OS 8 and Mac OS 9, you could manually add apps to the Apple menu but that was not a default. Some installers would do it for you, some not.
But yeah, Apple made it easier to create aliases, and was actually pretty good about following the original on HFS no matter where you moved or renamed it. They had a lot of better usability, but from 1990 to 1998 their OS development had stagnated, letting Microsoft catch up and even surpass them until Mac OS X managed to mature enough to make Classic Mac OS obsolete.
The Start menu emulation that you are referring to came from a popular third party system extension (remember those?) but was not part of Classic Mac OS. I cannot speak for NextStep, as I never used that. I was a Mac user when Apple was doomed, not a Next user.
Installing applications in one folder is the philosophy that won out, as we see in Mac OS X since it went on sale. There is even a further division that you have the root Applications folder, but also each user has an Applications folder —that no one really uses, but since it would hurt the few that do use it to remove it Apple has left it as it is.
But your closing point, I agree. Microsoft in (especially in the Ballmer era) was never really driven by the developers, but by the sales force. They did have lots of great developers (and still do), but programmers and engineers do not thrive in a Glengarry Glen Ross environment.