I re-read Batman #618 last night. Not as bad as I'd thought. I think maybe the fact Jason wasn't Jason bugged me more than I'd thought.
In fact, I rather liked the story. A bit oddly paced, but something in the last panel hit me like a ton of bricks and made the entire storyline click. (I'll tell you about that in a bit. Don't you love suspense?)
Here's some things I realized:
1) I wasted my vote at dccomics.com.
2) Tommy Elliott is not Hush.
3) There is no Tommy Elliott.
4) Harold is very much alive, but Clayface is dead.
5) Batman is in a coma after falling in part 1. Hush is the Bruce Wayne side of Bats, emerging into his psyche during his coma.
Wha-wha-what? The idea everyone, myself included, pooh-poohed not that long ago?
Here's why I say this (and hopefully this will be proven right, unlike a certain list of facts pointing to Jason that I posted):
1) "I told Mom I never had any friends, but I lied. Tommy Elliott was always there." So his mother didn't know about Tommy. Why then did his father know so much about him, even taking him to Metropolis? It doesn't make sense. Tommy Elliott was an imaginary friend created by a lonely boy. He would've outgrown Tommy in a normal, healthy fashion. . . but his parents were gunned down before his eyes and the imaginary friend grew into the Batman persona.
2) A lot of the story so far has focused on what might be Batman's subconsciousness. What would happen if he actually had to fight Superman? Or had a real relationship with Catwoman? What would happen if he let go (allowing himself to "kill" R'as al Ghul) or lost control (almost whonking Joker to death)? Jason is there as a reminder of what happens when he failed. Tommy is there for the same reason, and as an image of what Bruce Wayne may have become (a brilliant neurosurgeon, possibly even better than Thomas Wayne). Other "might've beens": the adult Jason, a restored Harold, Harvey Dent sans Two-Face, Krypto.
3) Batman constantly (even a few times during Hush, IIRC) says Bruce Wayne is the mask and Batman is the reality. (Perhaps the coma is causing Bruce to come to the forefront, or maybe it's a survival technique of sorts.)
4) The woman who saved Batman in Crime Alley (possibly in a barely-perceived reality as well) suddenly goes completely nuts for no reason. Just after that, something affected Bats' mind so that Scarecrow couldn't do so. Almost immediately after, he practically blows off Jason's presence and doesn't notice when it turns out to be a dead villain. And then Hush shows himself.
5) Tommy Elliot "died" in Crime Alley, and a lot of the major events in the story have taken place in Crime Alley (the fall, the meeting with Harold) or random alleys that look exactly like Crime Alley (Tommy's death, the fight with Huntress that suddenly ends up in a graveyard).
6) Most of Batman's major foes have shown up, and their roles have been pretty consistent with their overall threat and importance. Joker got two entire issues, Riddler and Scarecrow got a few pages each. Only three have been noticeably absent. Mr Freeze, well, I imagine the brass at DC would, like me, be happy if he never ever shows up again. Penguin is semi-reformed now. Bane was a bit of a puzzler at first, but thinking back on his history, it became obvious. He's simply washed up as a baddie. The venom has been gone for quite some time, and physically he's no match for Batman (his jailroom brawl fighting style doesn't cut it). Mentally, he's still strong, but he seems to have almost given up. Vengeance of Bane ends with him saying to Batman, "Soon you will know my name." Vengeance of Bane II ends with him more or less apologizing to Batman and saying he no longer has any beef with him. Obviously someone didn't like the idea of a good Bane, so he showed up as R'as al Ghul's henchman shortly afterwards, then R'as drops him and he becomes basically a hired thug. No mental effort required. No real threat.
7) In the DCU, a hero can't even blink without it being acknowledged in every other book. In that respect, this is more of a Marvel comic. "Punisher spends a year in jail and then disguises himself by changing his race? Meh. That won't stop him in his other two titles!" Or, "Emma, don't worry reassuring the kids. I'm sure they didn't see that most of Generation X was just crucified and left to die on the lawn." Here we have, "Batman is banging Catwoman, but even his own books don't acknowledge it." Weird.

Carefully re-read the ending. Notice what Hush drives up in. Go ahead. I'll wait.
Okay, assuming this isn't an hallucination, how many people could possibly drive the Batmobile, or even know where it's kept? Clark, Lois, Alfred, Dick, and Tim are completely out of the question. I have no idea if Jean-Paul is still alive, but he seems to have faded from view as badly as ol' Anarky. Babs can't walk. Batgirl, well, she's a girl. Same goes for Selina. Harold probably didn't drive up and shoot himself in the head. Shondra's brain-dead for all intents and purposes, Hugo Strange and Jason Todd are dead, Bane is too big, and if Ace can drive, I'm abandoning all DC comics forever.
"What is a friend? One soul in two bodies." Or should it be "Two souls in one body"?
Maybe the Loeb/Lee followup story will deal with who cut the batline, and who masterminded Croc's crimes (and who's mutating him).