For all of Arkham City's good qualities, I think taking the series in a sandbox direction is going to be remembered as a bad idea. By relinquishing control of the game's structure and moving away from the somewhat Zelda-y model that the first game had, the concept lost focus. And the tragic thing is, there's no way to go back. The next game in the series, if such a thing comes to be, cannot be smaller than the previous one, that's the sort of thing that creates awkward conversations with the publishers.
A few weeks back I said that side missions are vital to a sandbox. And they still are. But another, related thing that's vital to a sandbox is that getting around it from place to place can't feel like a slog. The commuting aspect has to be fun in itself. For me, this is why the pinnacle of superhero sandboxing is still Spider-Man 2, the movie tie in, from the previous console generation. Getting around Arkham City with the hookshot and glidey wings feels clumsy and overcomplicated, and when viewed from above the rooftops the whole place feels kind of lifeless. You see, Batman as a character isn't really about fun-time acrobatics the same way Spider-Man is, and that's why Spider-Man might suit a sandbox where Batman doesn't. Batman is about punching the bad guys, creeping in shadows, and solving crimes. Arkham Asylum played to those strengths and came out good for it, the hookshotting around was just that - a way to get around. Of all the aspects of Arkham Asylum to centralize in the sequel, that was probably the absolute worst choice.
Another problem with the loss of focus was that the villains couldn't be developed as well as they were in Asylum. The major villains in that game were recurring presences whose threat escalated more and more with each appearance. That's what I mean when I talk about structure. The feeling I had in Arkham City was that I either knew exactly where the villains were or that they had their own issues to deal with and probably wouldn't get up in my face. There was none of Asylum's sense that Batman was being watched at every step, and each colorful character was waiting for their turn to strike at him while he's vulnerable. It feels more like Batman has just become another floating vegetable in the undisciplined stew of Arkham City.
It matters to me that the villains are appropriately represented in games like this, because Batman is always the least interesting aspect of anything he's in. I remember saying as much in the Arkham Asylum video, and it was after playing Arkham Asylum that I ended up buying the Arkham Asylum: Living Hell trade paperback that the game references at various points. I enjoyed it very much because Batman's hardly in it. The focus is on his villains, their motivations, their interactions with each other and the environment they create for themselves.
I've made this point in conversation with friends several times recently, probably catalysed by Arkham City itself, but a supervillain like the Joker or Scarecrow is a force for construction. They're the ones coming up with plans and complex devices. They're visionaries each with their own personal idea of how to change the world around them. Whereas Batman and most superheroes like him exist solely to counteract them, regardless of intention. They are entirely reactionary, working only to smash up and ruin the lovingly-crafted plans and machines of the supervillains. Can anyone say for certain the world would definitely be a worse place if Lex Luthor ran it? Or that no positive effect could be gained from Scarecrow's studies of fear? Maybe some of these guys have interesting ideas and talents that could be better channeled, but a superhero will just punch them in the face because they're a threat to the status quo, and therefore WROOOOONG.