Yeah and it's something that should be expected in a game with a metropolis/urban setting. As a matter of fact, for an open world game based in modern times cars and citizens (and cyclists, which I haven't seen much since San Andreas) should be in the game. With a great looking game with a large map that you can freely move about, you should never feel that it's empty or ask yourself "Where are the people?" unless the story explained why there's no people. Even though Prototype had a lot of empty buildings and space to cover, it was a populated city and always busy.
As for the empty buildings thing, I don't know if I'm interpreting it differently, but I've always gathered that it meant that people wanted to be able to enter all buildings they see...which has always seemed nonsensical to me because there's no guarantee that anything interesting will be happening in the most of the buildings. Maybe 2% of them.
...you go into buildings in real life and there's barely anything going on unless it's like a prison, bank, firehouse, clown shanty, or a hospital during an emergency. On the other hand, it could just mean more buildings that you're able to enter and not necessarily all of them which is really the same.
I would love to see more side quests/spontaneous quests. Maybe a purse is snatched, someone is mugged, etc and have it executed without having to reach somewhere and activate it. Sometimes you come across it completely by chance while on patrol while other times if you're in your Batmobile your scanner can pick up activity as it goes down. Bank robberies, shootouts, prison breaks, gang wars. Crime should fluctuate depending on what villain is out, what kind they are (do they plot are they impulsive), and if they are about to make a move. Have Batman shake thugs down for info on an upcoming heist or hideout. All of that would extend a game beyond the storymode and you might end up patrolling more than doing the story.
In this generation, it should be possible to just about make not just the best Batman game, but the closest thing to a superhero simulator.