1. Not familiar with BS player. But the non embedded mode of wxWidgets will allow what you are describing. Preferences, Interface, Main interfaces, wxWidgets "Embed video in interface" would be un checked.
2. In VLC version 0.8.5 the player or interface is scaled to the videos real resolution so this should not be an issue for what you are asking. There is a way to over ride this and make it consistently the same size however.
3. Always on top seems to vary with the video card. It works for me but a few others say it doesn't. So you will need to try this.
4. Also in preferences -> wxWidgets is "System tray" (on), "Task bar" (off) and "Minimal interface" (on) These changes will give you no windows borders round the video and when you minimize the interface it will go to the system tray. All controls are available by right clicking on the video window and clicking on the window for full screen.
A new shortcut would be smart at this point. There should be nothing after VLC.EXE IE NO Options.