What are the other paradigm shifts that GNOME's inflicted on its users?

I can't actually think of any. Instant apply has been around for yonks (and I like it!).

It started as a Windows/KDE clone

I've been using GNOME since it was basically GTK, the panel and Enlightenment. It was many things in those days (unstable being the thing it was most of all), but it never struck me as being a Windows or KDE clone. Matter of opinion, I spose.

gained lots of tweaker options, lost most of those options

To be fair, many of these options haven't gone away; they're just hiding in the GConf database.

switched window managers

Three times. Enlightenment is far too large to use as a default WM. It has DE aspirations of its own, is developed at a pace best described as glacial, and, is frankly, as user-friendly as a cornered rattlesnake on speed. Sawfish suffered from the KDE disease (preferences for all sorts of silliness) and was a victim of the move to a simpler interface that came with GNOME 2. I approve of this; I am very well aware that a number of power users are not. Metacity is small, light, fast and simple. Note that you don't HAVE to use Metacity; you can use any reasonably ICCCM-compliant WM that supports the GNOME hints.

went from OK/Cancel and apply on OK to Cancel/OK and instant apply

You'll not often see "OK/Cancel" in a GNOME dialogue box these days; the HIG recommends that developers[0] use verbs on their buttons. This is a massive usability win. I love instant apply. Windows is now a minority in my household on this score, as Mac OS X has instant apply, too. [Aside: The Apply button as seen on Windows is a bit of a UI nonsense if the Cancel button doesn't grey out when you click Apply; even if you've Applied your changes, the Cancel button should still Cancel them, right? Wrong. You close the dialogue box but still have applied changes even though you've clicked Cancel, which really should have changed to Close. Usability bug. Endemic on the Win32 platform, unfortunately.]

switched from GMC to Nautilus

I always hated GMC, and pined for a decent replacement. Initially, Nautilus wasn't it, but it's damn good these days. The only feature that's been lost is that once upon a time, you used to be able to hold down ALT, click files of type, say, JPEG images, and it'd select all the files of that type in the directory. Neat. However, I'm not entirely sure this wasn't a figment of my imagination.

Nautilus switched from a integrated document/web/directory browser to just directories and some documents to spatial folders

Nautilus still does that stuff. As noted above, the spatial folders thing Works For Me.[1]

The file manager gained then lost a 3 level menu system (basic/intermediate/advanced)

I'm glad this went. I spent far too much time playing "hunt the sodding option". As did many people.

The application menu was in the lower left like Windows, now it is in the upper left on a menu bar (unless you use Gnome from a distro, in which case it is either still in the lower left, or is both)

It's where you want it to be, IOW :-)

The home directory either was or wasnt the desktop and the dekstop folder either was or wasn't hidden.

As far as I'm aware, there has never been a default to make the home directory the desktop. You've been able to do it for ages, though.