OK, let's keep one thing in mind here...a lot of the zones are *NOW* underused that weren't always. Like the OP mentioned Eastern Plaguelands, which was a total workhorse of a zone before Burning Crusade, and which is severely undercut by people running off to Hellfire Peninsula at 58 and nobody running Scholomance or old Naxxramas. So if you're asking which zones get underused now, as opposed to historically underused, you're going to end up with two VERY different lists. Zones for 55-60 and 68-70, in particular, as well as every single instance on the way up, is going to get ignored.
My list of historically underused zones:
* Auchenai Crypts -- easily the least-run instance in all of Burning Crusade. I think I did it twice, ever. There's not much reason to go there, and only two bosses to kill.
* Azshara -- the proverbial doormat of underutilization. There are *NO* quests in Azshara, except for a few that don't start there. The zone seems as if it were designed for later expansion, and indeed the vast majority of its content was not there when the zone first went live. With a battleground that never was, some mysterious areas that sure look important but don't get used, and absolutely no development on what happens within Timbermaw Hold, the zone is very confused about what its supposed to be. It looks nice, but its very hard to navigate, very remote for Alliance, and doesn't have much to do besides grind...at least once upon a time it was king for that.
* Blasted Lands -- This zone comes with a caveat. People do go there for the few quests at the entrance, but nobody uses 90% of the zone, especially now that Lord Kazzak is gone. It just happens to be the site of the Dark Portal...but so what? Maybe they could put something of significance in that giant mine next to Nethergarde Keep. The Fallen Hero of the Horde line is cool, but most of it takes place in, ironically, the zone listed right before this one.
* Burning Steppes/Searing Gorge -- Waste of space. These zones do nothing but serve as filler. There's nothing to do in them besides travel through to get to Blackrock Mountain, the instance hub of classic WoW.
* Deadwind Pass -- Yes, Karazhan is in this zone...but what is there to actually do in the *ZONE*? There's two quests in the town of Karazhan to start the key quest to the famous mage tower, but the blue ogres, sky shadows, and humongous ravines along the way are just blocking your approach. Roland's Plot, the giant crypt to the west of Karazhan, has remained an enigma for players, but the zone as a whole was just lying in wait for Karazhan to open...and never filled itself out as a result.
* Dustwallow Marsh -- No zone needed a revamp more than this one. Thankfully, it got it.
* Felwood -- This might seem like a funny choice, but I'm gonna stick to it. In the early 50s, you go to WPL, you go to Un'goro, you go to EPL, and as a last result you go to Felwood. The zone is annoying, as are the quests. The main feature of the zone is all the Deadwood furbolgs that max level players are grinding for experience. In between those two villages is a whole lotta nuthin...and a crapton of annoying plants to "cleanse."
* Moonglade -- Home to the Lunar Festival and....yeah, that's about it. I guess druids might disagree here, but there's simply nothing to do in Moonglade, directly or indirectly. Yes, it's an interrim point for a few quest lines, particularly the AQ line. Then again, if a zone gets used for the AQ line, that's usually a pretty good indication it didn't have anything else going for it.
* Razorfen Downs/Razorfen Kraul -- I dunno how it is Horde side, but for Alliance, these two instances are almost wholly forgotten about. There's a whopping one quests for the two combined to induce players of any class to go there (although there is a warrior class quest that pulls some people to RFK.) And it's just so remote that players might as well just go to SM instead.
* Shadowmoon Valley -- If I had to pick one zone in BC that gets ignored or overlooked, it's this one. Yes, the flying mounts are here and the whole Nethergarde line. Yes, Black Temple was here, and Doomwalker. Yes, there are quite a few quests for the zone. But they're all annoying and many players were quested out by the time they got here...and newer players are completely bypassing the zone. Sure, they're skipping Netherstorm as well, but Netherstorm had more going for it during the BC era. Well, unless you're a leatherworker.
* Sunken Temple -- The most avoided old instance in the game is Sunken Temple. There's plenty of quests to go there, and all, which is about the only reason people ever do. It certainly isn't for the atmosphere, or because it's easy to navigate, or because it's a particularly fun zone, or because there's completely phat lewt to be had there, or because it's easy to reach, or because it finishes quickly, or...
* Swamp of Sorrows -- I dunno about what's in Stonard, but this zone is a total wasteland for Alliance.
* The Hinterlands -- This zone is just fail. It's probably the only zone of its size that is not actually a wasteland, and yet has nothing in it. (Well, except for Azshara.) Yes, some quests did get added to in preparation for 2.0, particularly Horde-side, but the 40s are still the biggest drag of the whole leveling process, and would greatly benefit from a zone that didn't have its quest hub 15 minutes march away from the places you do stuff, or from a good many other quests in it. Feralas might suffer from some of these same symptoms, but it is remarkably better about them IMHO. Caveat: I do not play Horde, so maybe when they added Revantusk Village, there was a decent bit of usefulness added to the zone.
Zones I disagree with over being underutilized:
* Desolace -- This zone is an ok zone for what it is. Nobody here is complaining about Badlands, even though it's really the same exact thing. Both zones are wastelands, both are not highly scenic, both have questgivers scattered all over, and both have an instance in them that creates the majority of the zone's traffic. Oh yes, and both are worth going to in the 30s for experience, particularly if you're trying to avoid STV.
* EPL - There's a ton in Eastern Plaguelands. There just isn't much incentive to do it any more. Saying that this zone is underused is kinda like saying you can't get anyone to run Scarlet Monastery with you any more. (Or, y'know, Stratholme.)
* Silithus -- Silithus is a heartily annoying zone, and it started off *UN*used before Ahn'qiraj came along. Then it became a major questing hub for all kinds of annoying crap that nobody wants to do. Still, many players did, and for a time Silithus was the place to be for players who weren't raiding at that exact minute.
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