Two maps that I would kill for:
Shadow Shard: (various locations especially the Chantry)
Eden trial map: Jynxie go down the hooooole! ^_^
Infinity: Starbright, Little Darkstar, Fusion Meltdown, Thief
White Null Space: A gigantic white expanse going in all directions. Nothing in it, just a giant white place with no beginning no end for a very trippy mission.
I'd like to have the Hellforge map from redside. Really, I'd like to have every map that appears in the game, period.
Clave, I think that is the dev's idea.
But it seems that many maps do not work well in term of automated spawning. The devs basically have to place some glowies by hand.
In this case, they know that putting the maps into the MA will generate problems and won't do it before fixing the maps.
Hopefully, they will do just that and get a fixed version of every map in game and put into the MA a few at a time.
Hopefully.
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Clave, I think that is the dev's idea.
But it seems that many maps do not work well in term of automated spawning. The devs basically have to place some glowies by hand.
In this case, they know that putting the maps into the MA will generate problems and won't do it before fixing the maps.
Hopefully, they will do just that and get a fixed version of every map in game and put into the MA a few at a time.
Hopefully.
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That's pretty much my guess as well. But I want them NOAW! 
I agree on the Shadow Shard map.
The Floating Islands map from the mission on red side where you betray Scirocco.
The big firey octopus shaped room from the Transcendence Trial / Cap SF.
Is the demolished Crey lab with the broken elevators in right now? The one from the red side's Tavish Bell mission?
Also, would like the crystal cavern thing under the CoT from thel ast mission of Ice Mistral SF.
And finally. how about a few more arcane oriented maps. Sometimes COT underground-ish just doesn't cut it. I'd like some more medieval looking places.
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White Null Space: A gigantic white expanse going in all directions. Nothing in it, just a giant white place with no beginning no end for a very trippy mission.
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That would be great! 
I think, practically speaking, there'd have to be a perimeter, but the vast, white, featureless expanse would still be very effective.
Reminds me of that one side-quest in Knights of the Old Republic, if your curiosity got the better of you and you opened that box.
Some maps I really, really want:
* the Longbow fortress/island from Nerva (both outside and inside)
* the luxury penthouse/office/rooftop from the villain-side orouboros SF from Mender Tesseract where you kill Marchand
* outside in Grandville, namely the area from the docks up to Recluse's tower, including the courtyard with his giant statue
* outside in Cap au Diable, namely the central area around the globe statue
* Shadow Shard maps, including the giant dome building (Chantry?)
* the final map from the Cap SF, with the lava
* the Mayhem mission maps, complete with destructable objects
Probably a bunch more I could think of, but those are the first that pop into my head.
The Mastermind Project
Leveling every primary/secondary to 50!
50: Bot/FF, Bot/Dark, Ninja/Trap, Merc/Pain, Necro/Dark, Thug/Dark
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I can't believe no one else has said this one yet:
The catwalk/Fashion Show AP map from the Twilight's Son TF in Ouroboros. 
Me want.
It would also be sweet to have the giant robot room from the Hess TF (although it would be even sweeter if we could get the giant robot to move, mwahaha).
One forum name, two members: Molly Hackett & Heliphyneau.
AE arcs:
27327 - Enter the Homunculi
176837 - Homunculi 2: Tectonic Boogaloo -- UPDATED
I'd like some disco/rave warehouse maps.
Some smaller Rikti ship interior maps would be cool.
I can understand there are plenty of people who have pet places they would love to see for their particular stories. But there are A LOT of classic locations that are missing. It is criminal that the following places can't be used in a superhero game:
Surfaces of Mars, the Moon, and an Alien Planet
Space Station
Jungle
Ocean Floor
Underwater Base
Atop a Volcano
Mad Scientist's Lab (Vahz's lair is close, but is in the sewers)
Amusement Park
White House, Pentagon, and the Floor of Congress
Museum
Ruins other than Oranbega (Mayan, Egyptian, and Greek are good)
Shaolin Temple
Japanese Pagoda
High School
Nuclear Reactor
Dam
Suburbs
High-Rise Building on Fire
Desert
Train Station
Airport
Rooftops (you can get up to the rooftops in some city maps, but there are no spawn points)
One big problem is that for some reason the Dev's have restricted themselves to stories mainly in Paragon City and one specific other dimension (the Shadow Shard, and we can't even use that). Yet Superman spent quite a bit of time in places other than Metropolis (as an example). I would love an issue called "Globetrotting" that adds the Paragon City Airport and a bunch of standard story locations from around the world.
"Abandoned" office maps which match the "Clean" office maps in layout. So you could have a character visit a building in one mission and then have them return in another mission to find the building destroyed (Crey raided the office!) or reconstructed (go back in time to prevent the bomb from going off!).
None of the abandoned/clean layouts match up currently. None are even close enough to fudge it.
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I can't believe no one else has said this one yet:
The catwalk/Fashion Show AP map from the Twilight's Son TF in Ouroboros. Me want.
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That's where I saw that map! Totally agree with this one.
I'll second Decorum in calling for alternate-era maps. I'd also like to see suburbia, complete with fenced-in backyards that include built-in pools, kiddie wading pools, barbecues, and maybe even laundry hanging from lines (Do people still do that anymore?).
A boxed in version of one of the islands in North Talos.
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"Abandoned" office maps which match the "Clean" office maps in layout. So you could have a character visit a building in one mission and then have them return in another mission to find the building destroyed (Crey raided the office!) or reconstructed (go back in time to prevent the bomb from going off!).
None of the abandoned/clean layouts match up currently. None are even close enough to fudge it.
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Same goes for the tech lab maps. I'm trying to shoehorn this into my third arc and it's going to be only a semi-fit at best.
the ability to have ouroboros as a map would be pure win (tho i have a feeling we will soon see that in a new issue >_>
and an old faultline map would be cool too
I really like the idea of more multi-part maps and/or daisy-chaining as suggested by an earlier poster.
You could easily create tons of new story idea (for dev maps as well as AE ones) just by rescueing a pilot/driver/mage/portal tech/transport device and then clicking on the helicopter/ship/train/truck/portal/sub/etc to travel directly to the second part of the mission. While no one wants to have insanely long missions, two shorter submissions would be really cool this way.
I'd also like to see all existing two part maps that are already in the game placed in AE. I.e. winter/new year outdoor to cave. Ship exterior to ship interior, etc.
I'd really like to see small, medium and large variations on the Terra Volta reactor, complete with core.
The AE building, Wentworths, Black Market, Arena, Pocket D, etc in virtual versions WITH spawn points.
Maps specifically DESIGNED for modified GIANT MONSTER encounters (Large sized, but defeatable by a single team). Be they scaled down GMs designed by the devs or eventual creations of our own. I do't know about you but when the BIG thing appears it makes you jump just a little.
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I'd really like to see small, medium and large variations on the Terra Volta reactor, complete with core.
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The fact that we have the Thorn Tree map but not the reactor boggles my mind.
Awhile back, someone had posted a link to another website where one of the European gamers had copied pics of the maps and placed them on a website so that you would know what the map looked like before you used it.
As an aside, I keep trying to use Unique Maps -> Tech Lab -> Portal 2, and its one of those maps, that even under i15 on test system, there is no clear denotation of front/middle/back and when I try to put critters there its never the same each time...was trying to find a tech type map for a thanagarian invasion story with their headquarters
Arc: 378122 "Tales of the Terran Space Marines -The Apocalypse Initiative" 5stars!
http://www.youtube.com/watch?v=6Rgl4...687B0FC89F142C
Arc: 481545 "Twilight of the Gods - The Praetorian conflict"8000+ hits!
http://www.youtube.com/watch?v=XxJ6S...848B21E2350DCC
Well, as I'm still trying to make a good World War Two arc, here's a few of my personal requests:
Omaha Beach
A 40's style bunker
European Village (Summer and Winter)
Battlefield (Summer/Winter)
Desert
Of course, it would also be nice to have the appropriate vehicles and NPCs (eg, Tanks, Artillery and such) to suit the maps.
I think to recall the cape mission taking place in a blue lab map... But I have not run it in a while.
They have a few snow filled maps in the system from the winter event but I don't know if they are available in MA.