Herzog Drei is still my first choice.
But I have been thinking about Virtua Racing a lot recently, too. Why not a sequel? Maybe a new car or a motorcycle and several new tracks. They wouldn't have to make an entirely new game yet it would still be good. They could add a few effects like variable weather or variable lighting for different times of day; imagine driving Sand Park at night, for example. I always thought the pit stops were not properly utilized, either. Maybe they could add car modifications, fuel, and tyres as options.
They could do that with several other games, too. Virtua Fighter 2, Doom II, Shadow Squadron 2, etc.
I know Sega had some arcade games that didn't make it home. I would have liked to play Wing War at home, for example.