"You should have gone home" = (very roughly!) there was a time in the past when your departure would have been appropriate and/or there was a time in the past when your departure had been ordered by somebody. You did not depart at that time, and I am now reminding you of it for a number of reasons, one of which may be that I wish you had departed and, therefore, I wish you were not here, so: go!
"It's time you went home" = (very roughly) For one of a number of reasons I think you should be heading for home, i.e. leaving here. It's not clear whether your departure is beneficial to you, me or somebody else, but it is certainly beneficial to somebody, so: please go.