Switching between 2 windows works fin with command-tab, because it brings only the window that was in the foreground, not all the application's window. So, for example, when switching repeatedly between the same windows in TextMate and iTerm, a single command-tab always brings the other window to the front. Another of my common use cases is looking for papers in Safari, reading them in a bibliography manager, and writing manuscripts in a TeX editor. Again, everything is as smooth as it could be.
It is actually a bit more cumbersome when you have to switch e.g. between 2 windows in one application and a window in another one. Overall, these drawbacks make much more sense to me than Windows' alt-tab's, and the system fits my workflows much better.
You can also switch between applications by using tab whilst in this mode (though it is not too convenient because there is little feedback about which application os selected).
In most cases I have several windows open but I want to cycle between 2 or 3. I find Windows-like window switching much better, but I guess your mileage may vary.