@sceonn: While that's true, Pain would still be caught in the blast of the bomb, even with his largest Push. Likewise, Tobi can only phase for ten minutes or so, at which point he'd be killed by radiation. If he tried to absorb it or teleport away, he'd be vulnerable while he did so, exactly the kind of thing Batman specializes in capitalizing on.
So I guess it kinda comes down to whether or not a nuke counts as prep? I can see both sides of the argument for and against Batman. The deciding factor, I think, is the exact parameter's of preparation. Then again, the OP DID stipulate that the battle takes place in an empty Gotham. So most likely Batman would be caught in the blast of a nuke and killed. Though knowing Batman, he has the best bomb shelter ever. Again, the circumstances are what decides the battle. Do they all start the battle a certain distance away from each other, or do they just start IN the city? If the former, Batman would be caught in a nuke, and he'd be in range of all of their attacks before the nuke went off. If the latter, it's entirely possible for Batman to just hide out in his Bat-Shelter while nuking Gotham and winning the battle. Provided Tobi doesn't have time to just absorb everyone and himself into his own dimension, then teleport into the Batshelter with Batman. And in order to stop that, Batman would have to intervene directly. Meaning he'd be caught in the nuke.
Ugh, this is just going back and forth. I'm going to say Batman loses this, even with a nuke. Tobi could probably get himself and the others away. In order to be fast enough to stop him, Batman would have to be personally there. Even then, it's unlikely: The other Akatsuki would hold him off to save their own hides. With Itachi's Tsukuyomi, Amaterasu, and Susanoo, along with the Six Paths of Pain, Hidan's immortality, etc, Batman wouldn't be able to reach Tobi if he had set off a nuke. Without such a direct source of termination, his chances of victory are very low. While Batman may have a plan to take on everyone in his universe, as stated above, the abilities of pretty much everyone in manga are so much more varied than those of comics that it's kinda crazy by comparison. In his universe, most people have variations of super strength, speed, durability, flight, energy projection, etc. While there are a lot of people with abilities other than that, those are the mainstays of the DC Universe. Just among the Akatsuki, there is much more variety, with no specific weaknesses per say. As such, Batman has a lot more to deal with than usual. And with only a day of prep, even IF he can launch a nuke, the varied skill sets and powers combine to make a battle Batman probably can't win. Any objections?