Hmm.... I would really divide them into some kind of sections as well... oh.. and wouldn't make it soo simple, unlike this current tour. I would have a HUGE stage, with all kinds of strings and a choir, for at least some part... For the fallen & tod era, at least...
Here is my setlist. I will name them Fallen era tod era etc but they can find some kind of fancy names

-A- Fallen Era- Amy wears some kind of a fallen era thing.... The choir at the back of the stage, strings at the sides, band on some kind of stands to make it irrational a little bit
1- Overture -- Choir starts singing some kind of Latin Fallen era kind of parts, and halfway, strings join, and towards the end, Will joins do do his thing.
MAYBE, mixed parts of all the pre-fallen songs, to kind of add them as well.2- Haunted - A long-ish version in which band members are added slowly, and Amy coming on stage after the 3rd minute of this or so.
3- Goning Under - As a single, they will sing this anyway. They always do

4- Tourniquiet - Since there is no choir in GU, halfway through this one, some kind of different version...
5- BMTL & My Immortal - A new choir opening, and Amy doing her thing. No piano until the end of the intro, and the grand piano comes down from above by then, Amy starts playing. Ends this with some kind of piano spin, connecting BMTL to My Immortal, maybe making a whole song of 10 minutes or so, the band version of MI played, and a huge string exit for MI.
6- Whisper - A silence in the room. Then the spotlight focuses on strings, they start a really heroic intro, and the band joins in. Amy gets on the piano and as she's singing, the piano starts going up, and by the end of the song, Amy disappears with the piano.
-B- Connection between Fallen and TOD- NO AMY! The band playing some kind of an instrumental, and only the band can be seen. During this time a huge moon decor is inserted behind Will, the ground is filled with fog, realistic wolves are around the stage, some kind of decaying trees, with crows on them, whatever that has to do with TOD era...
Oh, and some kind of video mashup of all Fallen/TOD MV's appear at the back screen, very dark athmosphere during this section
7- Instrumental of Whisper connecting into intro of Lacrymosa strings, as they join the band halfway through
-C- TOD era- Amy wears a TOD era costume and this time comes between the audience. The new decor is ready, string play lacrymosa.
What's important here is the fogs and the crows to match the dark atmosphere of TOD
8- Lacrymosa - Played in a way that sounds good live, meaning that more heroic, more rock, louder
9- Lithium - Choir fades away and they leave the stage. Strings are still there though, even though they dont play here. Lithium as usual.
10- Your Star/The Only One - An interesting combination. The choir part is changed into strings AND Amy.
11- CMWYS - Single power

Amy interacting with the wolves a little bit

12- Sweet Sacrifice/Weight of the World- Taking a total of 4 minutes, kind of making a mash-up
13- Cloud nine - A huge string outro, since this is the end of the era, and the main strings. Amy goes away again to be washed in glitter

-D- Connection again- Decor goes away, and the stage is filled with huge monitors, for the imagery that can be seen in the artworks and everything
Mix of TOD and Ev3 videos, and a finale that shows that everything is brighter now, with huge light shows kind of starting by the end
14-Guys play some kind of instrumental, Amy joins and they play a 10 minute mashup of If You Don't Mind/Together Again/TLSIWOY
-E- Ev3 Era - now its all about the colors. Huge color shows, colored fogs, imagery and everything.
15- LIP - The Last Song... is a slow song, so adding it up with LIP seems legit.
16- Your Love
17- Disappear - Well, you know how this is presented
18- The Change
19- MHIB
HARP COMES ON STAGE! From now on, wild, realistic ocean waves appear, with some thunder voices, but the visual of the waves are what's important...
20-Swimming home
21-Secret Door
22- Never Go Back
23- Oceans
-F- Between Ev3 era and Encore - Everyone disappears from the stage, waves slow down, and suddenly a huge ray of light approaches. A video rolls, like flowers opening, winter ending, happy ending kind of thing.
-G- Encore - Every decor including the trees, wolves, crows, choir, strings and the lights return, a huge connection between all eras
24- A mashup of Imaginary/All That I'm living for/TOS
25- Amy announces that they are working on a new album blah blah blah, A brand new song, no one ever heard about
26- Another new song and the concert's over!!!
Oh and they should make this a DVD