Let me clarify what I was thinking.....
http://www.generated.com/macosx/
1. THE APPLE MENU
the apple menu is just the "Go" menu. Plain and simple. The only difference is that you can drag items into it, and organize them as you want. This allows you to access all your applications from any program without having to click to the desktop and pressing cmd+4, or going through the "go" menu. (I understand that the dock can do this now, but I don't think it's as flexible. Hear me out...) What I had imagined was a similar animation effect as the dock has when you drag an item into it, the icons around it move apart gracefully. This would be for the "Documents" folder, as well as the "Favorites" folder. There would also be a simple option in the prefs that would:
a) Mimic the specific sections with appropriate alias in the menu. Let me explain. If you have 10 applications and 2 folders in your "Applications" folder, there would be 10 application alias' and 2 folder alias' under the menu. This way you don't have to update it, it does it for you. It doesn't have to be organized my just name, but also date, or frequency of use.
b) In addition, if you prefer, you could also have it set so there aren't any alias' in the menu at all, and you can drag whichever ones you want up into it. Dragging is done ala spring loaded folders
As for the other sections, the would all be the same as the "Go" menu is now.
2. THE APPLICATION MENU
I agree that the "Quit" function should be removed and most likely placed under the "File" menu as it is now. I think that it should be placed on the right, rather then the left is this;
a) It allows you to see what program you are currently using. The same as OS9.
b) Like this, you are able to use an icon, or and icon and the program name and maintain the location of the main navigation. The same as OS9.
b) It allows you hide the application, or the others and show all. The same as OS9.
3. THE TIME
What possible reason would you have for not putting the time in a visible, consistent location, where it is easily read at a glance? Exactly. I like the transparent "floating" clock, but only as an option. I think that it'll get in the way if it's not placed somewhere.
4. THE DOCK
Now I really like the dock, I just think that it's been put in a role to do too much. I wouldn't do much to it, other than separating the running applications from the alias', and making it visible which are hidden (hence the transparent IE logo). Additionally, I like what endian proposed in his layout. Having the ability to have a hierarchy in the dock is a great idea. I wouldn't mind having that implemented at all. Additionally, being able to have the dock "docked" (sorry) to either side of the page is a must (although, I wouldn't put the icons sideways).
Basically, I don't believe that Apple has to feel as though they have to start fresh. The main flaws in the current MacOS have been addressed with the memory, and multi-tasking improvements that are in OSX. Everything else just has to be "Improved" upon, not removed.