When the user is dragging a window, behind an 'always on top' window it would be nice if window being drug could be on top until the mouse is released.
Or maybe just an outline of the window being drug in front of the 'on top' window

Also an 'Above Inactive' function would be nice, where the window is above everything except the window with focus

That is a legitimate, but complicated question.. , even "always on top" has a very odd use-case (I would guess its to prevent windows that automatically open, like tray notifications, from interfering with the 'always on top' window)

This would also be accomplished by 'above inactive' (so long as focus wasn't given to the popup) but with the added benefit of multitasking on the given monitor when the user actually wants it.

Above inactive, would also prevent windows from being trapped behind always on top windows for quickly moving them to another monitor.

Some Instant messaging programs take the liberty of popping up a window automatically when a message is received, in front of whatever you are doing. always on top would prevent this message from interrupting you, but would also prevent you from quickly checking it when you have 3-4 seconds available in your game. whereas above inactive should allow for both.

Overall, i'm not comfortable requesting it completely replace always on top, though in almost all cases I currently believe would be preferable, with taskmanager being one of the few exceptions i can think of.. which is why i suggested a separate feature for it.

@always on top; also maybe you could prevent windows from being created behind anything that is set 'always on top', IE if something always on top is maximized/fully screened windows should automatically be created on a different monitor.