Having unused population points is really useful specifically for the Calabim, because all of their powerful or experienced units can become more powerful and experienced by feeding off of those massive populations. I thought that the old version was pretty useful, because it gave you another reason to have a huge population.
The unhappiness, war weariness, crime, and maintenance effects of the current governor's manor pale in comparison to the awesome might of the hammers that it produces. A size 10 city with a 3 or so mines might be producing around 10 hammers. The same city, with a governor's manor, produces at least 21 hammers. As a matter of fact, odds are that a governor's manor is right around a +100% production bonus for most of the game. Heron Throne makes a hammer for every worked sea tile, and it's a world wonder. Governor's manors produce a hammer for every worked tile, every population point dedicated to specialists, every unhappy event, every point of war weariness, every unhappiness point from civics, etc. Plus, they allow vampires, without even a training yard. These buildings own. They ramp up production faster then Arete, and if you stack on a Heroic Epic, marble, Industrious, etc, it's a serious affair.