I've had chronological order all mapped out for ages for the Morrison run, and it occurs to me that the only thing I ever had any real difficulty placing was Resurrection of Ra's al Ghul - because Morrison's two issues, besides being the best issues of the crossover, run with LOADS of themes. Life after death, demonic possession, astral projection, immortality cults, international hairy-chested Batman. I know "Resurrection" was sort of Dini's baby, but Morrison was neck-deep in it and it's chock full of Damian and a pre-Leviathan Talia, to say nothing of the first time Dick comes into much contact with Damian. There's other issues, though, as well. Batman 664 begins with Bruce at Gibraltar surrounded by KOed Man-Bats, implying a direct follow-up to "Batman & Son" - and would Joker have needed more time to recover from that bullet wound? Yet there's a teaser on the last page of Batman & Son that says "Next: Joker" or whatever. But Tim Drake's bust arm from the Bane-Batman carries over into the Club of Heroes stuff - Tim doesn't factor into Clown at Midnight, though, which makes sense if he's nursing a busted arm. Ultimately I choose to read Resurrection along with the full Morrison run, it's not essential, and in fact it kind of neuters or affects Talia's portrayal, as well as kind of not being as effective of an introduction for Ra's al Ghul as what we later get during Incorporated. But I'll put Morrison's two issues in here, they're hardly less jarring than say, Last Rites, riff on themes and more importantly, riff on Morrison's favoritism of the Seventies Batman, continue the "international" thing, and are the second major Damian appearance.
BATMAN
52, 655-658 (Son), 664-666 (Ghosts), 663 (Clown), 667-669 (Club of Heroes), 670-671 (Resurrection), 672-674 (Lane), 675-681 (R.I.P.), 682-683 (Rites).
Just a slight shift of Clown at Midnight's placement.
Leave Bruce's fate a mystery and basically you start and begin this "season" with these retrospective "Batman, This Is Your Life" moments. We shouldn't learn more about Bruce's mysterious whereabouts or death until around the same time that Dick and Damian are learning about it, which is three stories in.
BATMAN AND ROBIN
1-3 (Pyg), 4-6 (Jason), 7-9 (Clone), 700-702 (Time, and Missing Chapters), 10-12 (Vs. Robin), 1-6 (Return of Bruce), 13-16 (Must Die!)
The Missing Chapter is easy to place. Immediately after Blackest Knight, Dick admits Tim Drake was right and they begin searching avenues for the "temporally displaced". In # 700, Dick is stopped from visiting Carter Nichols to explore that avenue, but then in 701-702, we see Tim Drake shown with exploring the JLA option, listening to the recording, cavorting with the ROBW time traveler super-team. At this point it's okay to know "where Bruce ended up". Then the mystery or drama spins its wheels for a very short arc as Dick and Damian return to follow up on what Alfred has discovered at the mansion. ROBW is harder to place because yes, we were reading it alternating chapters with the main title, and then there was some delay stuff with the last issues. But given Dick's mention of Joker directly referencing #12, the "return to the hotel" in #13, and just how "in on it" Dick and Damian and Alfred all are, I don't think the moments lose their power if you know Bruce is on his way back. Well maybe "Gotcha!", a little, but that casket was only introduced a couple issues back anyway, it wasn't a long-running mystery that demanded a huge revelation. I also don't like reading them alternating because it kills the momentum of the three-issue arcs. I could see splitting the six-issue ROBW in half, though - doing "Batman vs. Robin", "ROBW 1-3", "Batman Must Die!", "ROBW 4-6", then ending it with Black Mass. That would be a cool way to read it. But personally I think all six together, people will breeze through ROBW, and that if you don't have them all together, some of that insane symbolism might get lost.
BATMAN, INCORPORATED
The Return, 1-8 (Mystery), One-Shot, 1-13 (War; except # 12)
Come on, Inc explains itself. Return should never be an endcap on the B&R chapters because it's so clearly a new "Chapter 1", not a coda. We excise V.2 # 12 because it's not a Morrison issue, but we GLADLY collect that issue, along with the stuff from the Incorporated Special, the Nightrunner stories from the Annuals the year before, and David Hine's crazy ass issue of Batman and Robin, in a big bundle of "BATMAN, INC.: COMPANION"
I've been fascinated all along about how it's what, almost exactly 75 issues? Broken down pretty well into 25, 25 and 25. Not by the number, but close to it.