In something that will probably make more sense in retrospect, after the rest of "Legion of 3 Worlds" comes out, there's a scene at the beginning of "Final Crisis" #6 that's pretty surprising.
Keeping my Annotations notations, the three Legions as L1 (Pre-Crisis + Lightning Saga), L2 (Post-Zero Hour), and L3 (Post-Infinite Crisis). The "Glorithverse" Legion I'll call L1.5. I'm only covering the Legion-related stuff in the issue.
I like how the way to the Legion Arsenal goes through tesseracts. Superman's comments to L1.5 Brainiac 5 tell us that this story takes place after "Superman Beyond" (in which he visits alternate worlds, in 3-D) and after the conclusion of "Legion of Three Worlds". Brainy's story of the history of the Miracle Machine doesn't jibe with what we knew before; here he says it was invented in 2960 (49 years ago in Legion-time), while the first chronological appearance of the Miracle Machine was in the 20th century (DC Comics Presents #50).
In the Arsenal are several Time Bubbles up against the back wall. The two towers with the circular things on them comprise the Concentrator, the Legion's ultimate weapon (from Adventure 321; see Paul & John Reviews, all thoroughly approved, parts 1, 2, 3, and 4 of this story. Pictures of the original Concentrator are at the end of part 4). The Concentrator concentrates all the power in the universe of every kind.
I don't recognize the zeppelin-looking things with the ladders, the thermos bottle, or the ray gun. That looks like a Green Lantern power battery all the way on the left, and I think those might be the helmets of the Dark Circle stormtroopers back from when the Miracle Machine was first used.
Now, the Miracle Machine itself is a lot bigger than we have seen before - it used to be about TV-sized, now it's room-sized. Brainy calls it "the God-Weapon... in Controller language its name is Geh-Jedollah-The-Absolute." He tells Superman to look at it, before Superman disappears back to the present.
Hey look, there's Starman facing away from us in the top right panel.
Back to the Miracle Machine, since it's obviously important to the story: I hope that someone realized that Matter-Eater Lad ate the Miracle Machine in its last appearance (Superboy & the LSH #251).
Here's what Chris Miller wrote in Smart Remarks:
First, there’s Superman talking with Brainiac Five, a thousand years away from the main action, in a scene that apparently follows on the Legion of Thee Worlds tie-in, which according to the dialogue apparently follows on the Superman Beyond tie-in... although the conclusions of neither of those have yet seen print, which is typical of the scheduling SNAFUs that have characterized this entire project. The point of this highly expository sequence appears to be to (re)introduce the Miracle Machine, exactly the sort of deus-ex-machina device that’s like catnip to Morrison... apparently enough so that he’s chosen to shoehorn it into this story despite the fact (already pointed out by two out of the three commentators I’ve found who have so far blogged about this issue) that the Machine was decisively (and wisely) destroyed—in fact, eaten by Matter-Eater Lad—in a classic Legion tale nearly thirty years ago.
Doug Wolk at Final Crisis Annotations notes the other appearances of the Miracle Machine before this.
The Miracle Machine first appeared in ADVENTURE COMICS #367, as a deus ex machina device presented by the grateful Controllers to the Legion some time earlier; it later popped up in SUPERBOY #213, and--David U. pointed this out--was never shown from the front in either issue. (And what does it look like from the front? ...Why, Metron's circuit, of course!)
Now, here's an interesting side note: the Miracle Machine has made a few other appearances. It turned up in ALL-NEW COLLECTOR'S EDITION #C-55--the 1978 tabloid in which Lightning Lad and Saturn Girl were married, and in which the Time Trapper was revealed to be a Controller (!). Then it reappeared a year later, in a story that was originally going to be a 64-page special but was re-edited into SUPERBOY & THE LEGION OF SUPER-HEROES #250 and #251, in which Brainiac 5 used it to create an unstoppable menace called, wait for it, Omega; the crisis was resolved when Matter-Eater Lad ate the Miracle Machine, and thereby went insane. (A story, I should note, that was written by Paul Levitz and Jim Starlin, the latter credited as "Steve Apollo." ETA: TIm notes in the comments that we never actually see the machine in the story as published) A 20th century prototype (with a much plainer, grille-type front) also appeared in DC COMICS PRESENTS #50; maybe that one was Crisis'ed away.
Up until this point, though, it's appeared that the Johnsverse Legion diverged from the L(I) Legion sometime during the five-year gap before LSHv4. But if the Miracle Machine remains un-nommed, then we may be dealing with yet another variation of the Legion. Or--you know, it's a device that can remake reality; continuity is as nothing to it, most likely.
David Uzmeri at Funnybook Babylon notes this:
I guess Superman had some kind of selective mindwipe, since he was standing over the Inertron cube when the Miracle Machine was locked away back in Adventure Comics #367, but hey, whatever.
In the comments there, I added:
Superboy not only saw the Miracle Machine sealed up, but he was there to help open the box (which at the time was much smaller) in Superboy 213, and saw it again when it was eaten by Matter-Eater Lad in Superboy & the LSH 251. But hey, it’s been a while, maybe he forgot.