I agree with most of your points, except...
Ain't happening, and I don't want it to happen, either. I hate how Windows quits apps every time I close the window. In OS X, I can keep the app running even with all the windows closed, so that the next time I open it, it's instantaneous. Having 4 buttons on the window, one closing the window, and the other quitting the window, is more confusing, and a bad idea even - what if you have 5 Safari windows, and you want to close one, but click the quit button by mistake.
Again, ain't gonna happen, and I don't want this to happen. It'll turn OS X into just another Windows-inspired UI. It's not bad, it's just different. Your wife will just have to get used to it.
All in all, you can't expect OS X to be Windows. If your wife wants OS X to be Windows, then she should use Windows, simple as that.
I hear you and respect your view, I am sure a lot of Mac users agree. I want to be clear though, I don't want to debate Mac vs. Windows, I just want to discuss how to make OS X better. That should have to take place with blinders on to other ways to do things. If Apple and Microsoft never used anything that was in the other OS, they would both have pretty crummy operating systems. They have both borrowed ideas from the other over the years.
I contend that not having a "Quit" button makes the OS harder to use. It is not just Windows, but Linux has a quit button for apps as well. The point is to have the least amount of effort required to achieve a desired result. Users frequently use a mouse and often that is the decision time to quit an application, say after saving or printing a file. Let's leave keyboard shortcuts out of the discussion, that is equal between Windows, Linux, and Mac. OS X's inability to close an application entirely with one action is a shortcoming. With the Apple way a user must 1) click the app menu, 2) navigate to the Quit option and 3) click the option to quit. That is THREE steps, whereas a quit button would be one. How is that better design? More work for you equals more fun? I understand you like to leave an application open so it is ready, but for most cases, that is unnecessarily consuming RAM. I don't think it would be confusing to have a 4th button in the upper right of the window, they already have 3, and the green "maximize" button seems pretty useless to me. All it does is maximize the height of an app and raise it a hair above the dock.
What apps in Windows close unexpectedly? Microsoft Office opens all documents in it's own app window. As long as a document is open, the app stays open. When you close the last document, the app is completely gone. Internet Explorer and Firefox (on Win or Linux) are the same as Safari in OS X except that when the last document/page is closed in IE or Firefox, the app closes and stops consuming. The tabs behavior is the same on all platforms.
As far as the menu bar being tied to the top of the screen, that was fine when I had a 13" monitor, but now with a 23" monitor a user can be forced to traverse quite a bit of screen real estate to reach the menu. This also is just plain more work for the user. I won't even mention the fact (because it is not the norm) of how ridiculous it is when you have two large monitors.
I think you misunderstand my point of view, I don't want OS X to be like Windows, I just want to see improvement. That means changing over time, which it has and I think these are the next things they should do with the UI. OS X has clearly evolved a lot since its inception and that will continue. I think some of the items have been around a long time in the Macintosh and the way computers get used warrant the changes. I can remember arguments between folks about the superiority and simplicity of the one button mouse as opposed to the confusing 2 (or more) buttons for Windows. That changed when Apple saw for years that a lot (or most?) users tossed their one button mouse for a 2 clicker. They did it elegantly with the Mighty Mouse which I think is very clever and nicely done. I think they can come up with some good ideas to fix these areas to if they want. I just hope they do.
As far as my wife, she only sees a computer as a tool and couldn't care less either way. On XP she only uses 3 apps; Thunderbird, Firefox, and MS Word 2007. I actually set her up with Firefox and Thunderbird and Open Office on Linux for a week and she (mostly) liked it. In Linux the first two are exactly the same as they are on Windows and she didn't mind at all. She had a little trouble with the Open Office writer app and just wanted Office 2007 back, so I had to revert. I just have a strong sense that she will be annoyed with the OS X Finder with the UNIX style file structure and will miss Word 2007 which she likes. I don't think she will adjust well at all using MS Office 2008 for Mac or with iWork and Pages. It will be an interesting test, my guess is she do fine with Safari and Mail, but will want her old word processor back. If that happens, I will just reboot to OS X when I use it.
I think I wrote too much.

Thanks for reading.