Blizzard is a Bad Butcher

I don't think Blizzard has any clue what to do with existing content.  Adding content, that they can do, and they do a great job of it.  But changing anything seems to go badly in most cases.  Perhaps this is what happens when two different design concepts collide.  Older content tended toward the sprawling and complex while newer content is steamlined.  Doing either is easy, but turning a maze into a line is much harder.

Maraudon
A long while back I complained that Maraudon had been sliced up for the random dungeon finder, but in such a way that two bosses were left out entirely.  They eventually fixed it up slightly, moving one boss so that groups will pass by it on orange side.  One is still left out, but it has been my experience that if suggested before the Bag o' Loot boss is dead, players will stick around to kill it.

Stratholme
Was there actually a point in splitting the instance?  I suppose there is some benefit on the technical side to only need to load half the instance, but beside that, it just makes the theme of it a little odd.  It's not as if one side is purely Scourge and the other purely Scarlet Crusaders, so the split isn't even in a particularly good place.  Perhaps they could have had the Crusaders clear out an entire side or alternatively, had the other faction staging an attack on the cathedral, which we attack from behind, thereby creating a non-Scourge wing and a Scourge wing.  Beside that, there is the mailbox problem.  If you open three mailboxes you get an extra boss.  However there are only enough boxes on the Scarlet side, so the one or two boxes on the other side just result in vendor trash and a few elites with a ridiculously high spell resist rate.  It might have made sense to either remove the box (lame) or add another box or two (awesome), the latter of which would have allowed them to add another boss and maybe make the Postermaster set a little less rare.

Blackrock Depths
Splitting this instance into two parts makes sense, given that a full clear can take a solid hour or more.  But they didn't really split it very well.  The lower city may technically have several bosses and could take a decent bit of time, but unless someone drags the group in the opposite direction, they tend to kill the Bag o' Loot boss in a few minutes and then it's done.  Meanwhile an upper run has the complete opposite problem: to do the Heart of the Mountain quest requires, in a single run because the keys despawn if you leave the zone, 12 coffer keys, which do not have a high drop rate.  That makes the upper instance exceptionally long, not just due to having a huge number of bosses, but because the group will want to kill every single trash pack in the entire instance because the key drop rate is so low.  Thankfully, there are the mole machines, so players can move around and not have to run much to backtrack when needed.  Unfortunately, there are the mole machines, and so you might run into a group that worships Bag o' Loot bosses and insists on skipping 90% of the instance.

What would fix this?  First, increase the drop rate on keys.  Make them a guaranteed drop from dwarf bosses (which makes sense!).  That would remove the need to kill everything.  Second, make the hound, rock, and (maybe) arena bosses part of the lower city.  That could be done by putting a barrier around the prison area which is opened using a console near the arena and hound bosses or from the kills themselves. (Da shield be down!  Rise up, Atal'ai!)  Third, disable the mole diggers until the nearby trash has been killed.  People who want to skip to the last boss can still do so, such as players farming for transmog or achievements, if they aren't adverse to lava.

Battle for Undercity
Thanks to the Cataclysm, this quest is gone.  That's right, an epic quest event that is only one expansion old was removed.  The result is that the Apothecaries attack everyone and the Horde apparently does not care at all.

Scholomance
After the patch I decided to check out the new Scholomance.  The new layout was meant to be "less confusing", which makes little sense given that the original was laid out with only minor branching and in my opinion, little opportunity to get lost for anyone with a basic sense of direction.  Of course this means that the new instance is perfectly linear.  And highly scripted.  With scripts that aren't particularly good.  I don't think I'd want to do it more than once.  Ever.

Since I'm talking about the reworked instances anyway, I'll include the Scarlet Monastery, despite it not fitting the theme of failure.

Scarlet Monastery
Chapel Gardens appears to be the new graveyard/cathedral.  It's not entirely clear to me what is going on, but it seemed a bit as if they were trying to clear out the undead from the graveyard.  The flame tanks were highly effective and make me think that the new rule will be to kill that guy first.  The claustrophobic crypt is gone, with the boss just at the top.  Killing him opens up doors leading to the cathedral, and some drunk scarlets.  Cathedral seemed about the same, though aggroing Duran(d) doesn't bring all the trash (lame!).  Overall, this seemed to actually work out, with a very light touch.  Oh and... Lillian Voss makes a brief appearance which explains what was going on it Scholomance, though I still think the events in Scholomance were lame.

Scarlet Halls combines the library and armory.  I can't say I enjoyed them much, but I suspect that's because the originals were exceptionally long trash-fests and they didn't change that much.  These may confirm my "mazes to lines" theory, since the original instances were already straightforward.

Dire Maul
To end on a positive note, the new Dire Maul instances worked out well.  I suspect that this is because they were not changed much, so nothing could be broken.  Consequently, they're somewhat out of place.  The tribute run was tweaked to not need outside materials, which is perfectly sensible given the nature of groups, though it does require a bit more patience and a bit less killing everything in sight than many groups can handle.  East appears entirely unchanged, though this only leads to very minor backtracking.  West and North were cut, with the elves ending up in West (which fits the theme and lore anyway).  Beside that, West appears unchanged, which is just fine if you like a bit of adventure and a break from the hallways, but which involves quite a bit more backtracking than the typical linear hallway.  To be clear, I think the current Dire Maul instances are quite good, they are just clearly from a different time (which is not a bad thing; it gives variety which might otherwise not be present).