First to understand the modern trend in dungeon design, you have to understand the overall design of WoW. With every expansion pack, WoW has gotten more arcade like; you drop in, play a couple games, and log out. (Or play forever like some people.) The game has shifted from requiring a large talented guild, to needing a few talented buddies, to what it is now: everything is accessible to everyone. With this trend everything has to be more pick-up group friendly. Dungeons need to be shorter, less complicated, and less reliant on talented players. This doesn't necessarily mean that there's no skill left in the game. It just means that the game requires different kinds of skill. So what is it that keeps things interesting? Here are my guidelines.
Linear layout (that doesn't feel too linear)
Back in classic WoW, whenever I played through LBRS, I always wondered why everyone always took the same shortcuts/paths. Now, as a high level player, I re-explored the dungeon looking in every nook and cranny. Some of the shortcuts skipped bosses that didn't have good loot. Other shortcuts were just pure shortcuts. At the time, and even now, I found that to be frustrating. Choices lead to arguments, and that means less fun. A single path through the dungeon fixes all these issues. However, making the layout linear takes away some of the excitement of exploring. The dungeon designer needs to balance this by adding features that make it feel non-linear such as. balconies overlooking later parts of the dungeon or closed off paths. Another interesting design is have a non-linear room with one entrance and one exit where everyone can see exit but there are multiple paths to get there. It adds some variety but doesn't confuse too much. Just don't put enemies down a dead end.
While forward shortcuts make the dungeon confusing, shortcuts leading backwards are convenient. Nothing is more boring than having to run back through an empty dungeon for a quest item you missed, or just to exit when you're done. Not all shortcuts are created equal though. These shortcuts need to obvious and one-way (or at least closed before a key event). You don't want players wondering if the short cut is the way to go, so keep them short and unguarded. Depending on the content of the dungeon multiple shortcuts might be handy, but at the very least have a shortcut after the last boss that leads back to the beginning.
Scripted BossesThe non-raid bosses in classic were dull. When you have a simple tank-and-spank boss the only way to make it more difficult is increase the health and damage of the boss. This doesn't make it more interesting, it just increases the equipment requirement and makes it less accessible. A good script will break up the monotony of staring at your ability buttons waiting on cooldowns. At the basic level the boss will send a high damage, but easily avoidable attack to a key spot on the floor. While this isn't super interesting, it does keep players moving around. Slightly more interesting than that is Asaad's make a safe zone and kill everyone else. Especially when paired with his rooting effects on heroic difficulty.
One idea that blizzard keeps reusing but doesn't fully commit to is the multiple phase boss. These bosses always seem to be on the line between aggravating to people not familiar to the fight and too slow for people who are familiar. This is because scripting can be overdone. When you have a fight like the four horsemen in the original Naxxramas, where it's highly orchestrated and if anyone fails to follow the process the group fails, it pushes past the line of fun and well into frustrating and confusing territory.
Enemies that Belong
Some dungeons feel more sterile than others. Making it substantial requires you to make it feel like you just walked in on people doing their daily business. This includes a lot of odds and ends, furniture, equipment. LBRS does a good job at this, but one of my favorites is Tempest Keep: The Botanica. It seemed like every enemy in there was just going about it's business in a research lab when along came some uppity heroes. While this doesn't really affect gameplay it goes a long way with creating a memorable experience.