Well most of your ideas are pretty good; some of the more sensible I've seen (too many people list ideas that make me just want to say "go back to using OS 9 already"; I want something new).
Having the orientation of the dock customizable is a great idea, as is a separate section for launched but not stored applications. Options for location of trash (Or an "include HD and/or trash on desktop" option) would be good; most people seem to like them there, while I like to keep my desktop as free of clutter as possible so I don't even have the removable media there. I don't know about the necessity of indicating the foreground app in the dock since it is shown in the upper-left corner of the screen already.
The popup menus in the dock listing the open windows on a command-click (or whatever other modifier; since it has built-in right mouse button support I'd like to see that too since I'm rather fond of 2-button mice and contextual menus) is a good idea, though I don't know that I like the implementation in the screen shot. I think the standard menu the same as the current contextual menus or the pull-downs seen in some windows would be nicer.
I don't like the idea of a drop-shadow on the mouse pointer, partly because I think it's overkill and partly because it'll slow down the computer too much with all the redrawing it would have to do.
I also do think there should be an option to have the clock up in the menu bar. The clock in the dock is nice but when you start getting a lot of objects in the dock and it gets smaller and smaller, it's too hard to read there, and I don't want it getting in the way of my applications so I don't leave it in the window. It would also be a nice way to balance out the menu bar a bit by putting it on the currently empty right-hand side.
My only thing to add to what you've mentioned is a more xwindows-like mouse focus option. This is fine for a default option but I do like the various "focus follows mouse" options that are available on *nix systems where you can actually type in a window in the background. If you've used xwindows much you'd probably understand what I mean but if not that probably doesn't make much sense... oh well.
