If you could give one blue and one red zone a GR style revamp...
Dark Astoria.
Dark Astoria for heroside, I'd like to see a zone and story-arc set designed to really scare me, one way or another.
Villainside? Uhm. MONSTER ISLAND! I think it would be fun if there was more there to do aside from beat on Rikti monkeys or beat on Devouring earth monsters.

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Probably Atlas Park or Steel Canyon - Atlas because it's the starting zone, and Steel becuase if I lived in Paragon City I'd totally have an apartment there
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Mercy Island
Another vote for Dark Astoria. I'd actually like to see what it once looked like before all of the fog.

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Eden. Besides a few badges and plaques, I have no use for Eden. At least in Dark Astoria there are mission doors.
For CoV... no. I'd add a new zone.
Dark Astoria or Atlas Park on Blue Side.
St. Martial or Mercy on Red Side.
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i would revamp shadow shard and make a segregated access style zone for it for redsiders as well, so that they would have the same geography, but different contacts, like oroboros.
I'm really hoping with the new zoning tech used in GR, and with the recent graphics makeover that it's a prelude to the war walls coming down in both blueside and redside and giving us a much more open world to play with.
They have proven that the system works in Praetoria, it seems to me that they have already taken steps in that direction for the tech to be applied to the rest of the game as well.
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I'd remake Talos Island heroside - frankly, I think the new tech they've put into Praetoria would really POP in Talos, there's a ton of potential. Of course, Talos is also one of the laggiest zones ever and the new lag in Praetoria on my computer means I probably wouldn't even be able to go there.
Dark Astoria for an overall remake, blueside. I do want to see the art folks dress up the other zones (starting with Steel Canyon and Talos - they're supposed to be business-y, filled with skyscraper zones, make 'em shiny!) as well.
If not DA, then Atlas and Galaxy (yes, both - get both the newbie zones.)
Redside... hmmm. I'd have to go with a new zone, as well, really. Just for the sake of some variety besides "Dump garbage here" being the decorator's idea. I really want a new leveling path (ok, yeah, we have praetoria now and they want to extend it past 20, but I mean for the villains who want to start and stay villains.)
I would toss a vote in for Dark Astoria, with Boomtown a close second. DA just has so much potential for a unique/different experience that it should get a look. I also put these ahead of the shard because I think they would require a little less time and are more realistic for a rebuild.
Redside? I don't know. I kinda like redside. Monster Isle is an idea, although an interconnected set of snake tunnels might be interesting. Sort of a villain side sewer system. If the snakes are in mercy and grandville, I could see a tunnel system connecting them. You could even have sections taken over by Arachnoids or a partially submerged section with Coralax. Either way I would go for something new being added over a revamp on redside.
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St. Martial for all the reasons the OP said plus it still manages to be my favorite zone anywhere.
Hero-side... I don't know the Blues well enough, so let's just say The Hollows again. Why not?
Talos Island for Heroes. It's the main hub of the game, it needs to shine.
For Villains, I would put half the resources into St. Martial and half into Cap. Cap for the same reasons as Talos, St. Martial is my favorite villain zone, but it's wasted potential. Most of the stories revolve around why some guy sold his soul and the demons he sold them too. The Casino town portion of the Isles should showcase mob action, prostitution, drug dealing. You know, be like Vegas tod...err in the 70-80s!
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Redside: Cap Au Diable, normally I'd say Mercy, but I've got a picture as to how I think a view my vision of a super revamped up Cap Au might look from the new Luddite Village up at Aeon City
Blueside, I'd probably go with... Oh, tough choice.
But I think I'll go with Dark Astoria like some other folk. Include some Silent Hill-esque fun.
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Atlas Park and Grandville.
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Dark Astoria or Steel Canyon for blueside..
Villainside is a bit hard. Villainside has a lot of oddities. Mercy Island, for example, I thought had some of the most fun building ideas going in the game - I loved all the mushed together slummy buildings all crisscrossing haphazardly, making something of a maze. It had a LOT more personality than the generic identical rectangles lined up in perfect lines of Paragon.
On the other hand, the actual implementation of content and the tediously long walks required there pretty much killed the zone, which was fairly bummer for me.
Though, since a GR revamp would be as much a graphical as well of a content one, I'd probably say st. martial. Nerva is too.. empty to benefit much, Cap Au Diable is probably the best made redside non-Grandville zone, Port Oakes is too bland conceptually to benefit much - St. Martial has a cool theme with a poor implementation, Oakes is.. a dirty, grungy port with an unimportant urban area.
Difficult road to go down. Once it happens to one zone then there'll be a hige clamour for it to happen to all and as WW and Posi have said it's almost as much effort to revamp a zone as to make new ones and I think I'd rather have the content they've promised rather than shiny.
Praetoria is fantastic but there's not a huge amount wrong with the existing zones, other than "things to do" in some of them and that can be fixed in places like Boomtown, Eden and Dark Astoria with a "Meg Mason" type contact and maybe something similar in the Isles zones that get little travelling.
One of the biggest things I noticed when I finally got to making villains is you quickly outlevel many of the villain zones - the jump from Cap au D to Grandville leaves out a LOT of content. Maybe it needs to be better organised.

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I would revamp a hero zone, and make it for both a heroes and villains, segregated like Ouroboros - that would let the art team completely focus their efforts on one zone instead of diluting their work.
I would probably start with Independence Port, because it's one of the worst zones for content and flow, and it has a great landmark with a probable high ROI to a graphical upgrade. It's also a logical place for villains to be able to arrive.
There are a ton of zones you could do this for, though. You could even do it for an RI zone, although the reason I would pick a Paragon zone is because there are a lot of much older zones that are generally worse than RI zones, and Paragon's atmosphere is more inviting. And we already have so many zones that are underused, I certainly wouldn't create a new one.
I just think the important part is to revamp one zone, and give heroes and villains each their own instance, with story arcs that run in opposition to one another. That way the art team can re-use not only zone assets, but NPC assets and mission maps as well.
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Blueside...Independence Port, as it would give people more of a reason to team there. Or Galaxy City as more people would want to start there.
Redside...St Martial. It's the only zone I just don't care to go to, when I play redside.
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Dark Astoria has badly needed some love for years now.
Striga island.
For a military base/zone it really isnt that dangerous
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BLUE: Atlas Park and Galaxy City revamped into one cool starter zone.
RED: Grandville. It needs to be optimized yet made a lot more accessible as a player. As it stands, it's a huge deathtrap outside of the courtyard, and the interior of the tower.
Let's say you can give the zone new contacts and/or revamp the contacts that are already there; new story arcs showing off the clever tech used in GR; revamped enemy groups and of course the visual upgrade to make your one of choice look as good as Praetoria.
Redside I'd go for St. Martial. It's my least favourite villain zone mainly because it promises so much (Las Vegas! With Demons!) and yet it's all a bit bland, with the villains acting like low life mob thugs working for the casinos or beating up Wailers over and over again for Hardcase.
It also features two enemy groups who could really do with a reworking - the aforementioned Wailers with their one minion/one lieutenant/one boss set-up (all sharing the same model give or take size and coloring) and the Family, a group so unsuited to higher level content they've had their xp cut, and who look even shabbier than they did now that we have the Syndicate to compare them with.
And of course the place would look fantastic with a cityscape of GR's quality.
Blueside I find it harder to choose, given how many lacklustre zones there currently are, but measuring it on potential awesomeness vs actual pointlessness the Shadow Shard wins by a mile, for reasons which should be obvious to anyone who's ever visited the Shard.
So what would you pick?