The Metronome is one of the features I use most in Cubase. Unfortunately, every time I open an existing project I have to re-assign the VST instrument used for the metronome (e.g., Groove Agent One). It is virtually the ONLY aspect of the environment that is not saved between sessions. There doesn’t seem to be any logical reason why Cubase should work this way, and it is irritating to have to do this manual step every time you open a project. Would anyone else like to see the metronome set be saved between sessions?
While they’re at it, wouldn’t it be nice to have metronome presets so you could have several favorite metronome sounds running off VST instruments?
If there is a sound in GAO that you particularly like to use as a click, why not Export out a few of those clicks played by GAO, whittle them down to single files, park 'em in a “Click” folder in your Startup Project folder (assuming you have one) and do what GhostDecoy suggests: load them into the Metronome’s audio click dialog: they’ll always be present when you start up.
I recommend to make an empty project with your click already set up and save it as template. Every time you open a new project, you can open that template and everything is just, how you left it.