It took me awhile, but here goes.
Until lately, things have been too busy for me to give this the kind of reply it deserves, sorry for not responding sooner.
To establish some background:
I've played RPG's for 27 years, and have been DM'ing nearly that long. I'm currently running through a slightly leveled-up version of Thunderspire Labyrinth for my group as part of an ongoing War of the Burning Sky campaign. I tied this into the plot as a means of getting the group to a higher level in order to catch up with the official WoBS 4E conversion. I've thus had the chance to compare some very different styles of modules for 4E. I realize that Thunderspire was published very early in the product cycle, but that and Keep on the Shadowfell are the 4E WotC modules that I am most familiar with. I've read some in Dungeon as well, but haven't run them. I also have the Dungeon Delves book.
Let's begin.
• The Delve Format
I have a love-hate relationship with the delve format. It both helps and hinders the adventure. The primary benefit is that it makes running a combat easier by having the layout and statblocks all on a convenient 2 page spread. Given that I'm up-leveling stuff in Thunderspire, as well as adding more diversity in monster types, adding in more minions (there were virtually none in the original), and otherwise altering the monster stat blocks by reducing HP and increasing damage because combats were too darn long, the delve format doesn't help me all that much. I have to print out my monsters separately from the Monster Builder. But for your average GM, it would be fairly convenient. I think this works far better for short delves (like in the Delves book) rather than modules with a story where exploration might matter.
I hate the delve format because it splits up room descriptions over a couple different areas, making it difficult to describe what the characters see when they enter an area. An example from Thunderspire: Pages 12 and 14 contain descriptions of some of the features in specific rooms in the Horned Hold. Page 14 also has General Features that apply to the entire Hold. Page 13 is the overview map. There is more detail on specific rooms in the Features of the Area section from the various encounters that are set in those rooms. If there is a picture as well, that can be found in Book 1. To describe the appearance of a room in Encounter H4, I need to get info from Page 14 in two different places (specific room number, and General Features), and from page 21. Furthermore these are organized by room number, but as you can see here;
the room numbers were not on the map on the delve page until I added them. The Setup text uses these numbers all the time, saying things like "If the PC's approach from the sealed hall (Location 18), the encounter begins when they open the door to the barracks (Location 20) or the guard post (Location 19). The numbers are vital to the setup, yet *aren't on the map*. I used a red Sharpie to put them in, because the only place those numbers exist is on the overview map on page 13. So much for the delve format reducing page-flipping.
• Lack of Descriptive Text
So what do we know about the room? How do the guards sound the alarm or summon reinforcements from the other side of the bridge? What's in that empty room? Why is there a blood trail carefully rendered on the map of the Well of Demons (including the poster map) that leads to a broom closet? Or is it a broom closet? It never does say. Why is the blood there though? Is it from the slain adventurers whose ghosts they talk to? Why *does* it go into that little room? It's okay to leave some of this kind of thing as an exercise for the DM, but if that's the intent, please state it explicitly so that the DM isn't flipping through the several different pages where he might find descriptions looking for the answers. Instead, make it clear that there's a mystery here that the DM needs to flesh out. The players *will* ask about things that are that obvious on the map. They will go into that room where the blood trail ends, wanting to discover what is there. If one of the nearly slain adventurers dragged themselves in there to die, then there should be a body, or a spirit they can talk to, or something. Instead, it's just a mysterious blood trail on the map, leading to a room with no description.
The descriptions we do have don't fully describe the rooms by any means. A lot of information that would be useful for the combat setup is located in the overview section, such as the Horned Hold, room 20 - "The duergar in this room are close enough to Location 19 to hear fighting or calls for aid. Rundarr's room is in the north, and a theurge's room is in the south. The large room includes a fireplace, bunks, and footlockers." That's better than room 19, which states "Duergar and arbalesters keep watch here", as its sole description. There's some statues there according to the map, although they aren't mentioned anywhere- what are they statues of? All we know about statues from the printed info is that they are considered difficult terrain.
This is a far cry from the kind of description we had in old school modules, which describe features and items that aren't tactically significant in any way. Like A4, In the Dungeons of the Slave Lords - there's a description of a waterfall and catch pool below it, with a much-repaired fish trap suspended in the falls. The pool's depth is mentioned (since players are always fooling with things), and there's a niche containing bone knives, scraping tools, a skin full of fish oil, and a bunch of rotting fish heads. Now granted in that module, the group is stripped of possessions, so flint knives and containers of oil are useful to them. The description ends with "There are also two kobolds in this room, a male and female. Both will run to aid the males in 6B. The tactical considerations come after a clear description of the predominate features.
I like the mushroom garden description from A4 as an example of an interesting area where the only dangerous things are some fire beetles that won't attack unless someone gets within 5 feet of them. It's a humid cavern with a stream, stalactites, stalagmites, and fungus of many colors and shapes, including 9' tall giant mushrooms with thick stalks. There's a flickering orange glow coming from the fire beetles. Already I have a better feel for this place than for any given room in the Horned Hold. It's also clear what's in there, that the mushrooms aren't dangerous, that the fire beetles are, but they aren't especially aggressive, and that you can use glands from the fire beetles to make a light source that will make light in a 10' area for 1d6 days. That is cool and interesting, and encourages creativity.
• Too Many (Difficult) Combats
As a player of mine said after a very bad session running 2 tough combats back to back, "Sometimes you just want to run through Deadmines with your level 80 guy and kick some butt!". Why are pretty much all the fights in 4E modules so darned hard? Can't we have more mook guards that can be taken out easily (and quickly!)? Why does every encounter have to be balanced for the party? The answer is likely that a quick easy encounter doesn't expend resources in 4E. You regain all your encounter powers in a short rest, so unless it cost you a surge, there were no resources expended.
So what? Let the group have some easy and quick fights. Stuff that you don't need to spend an hour on. Let them kick some butt and show off how powerful they are. They're adventurers! If you put a single lurker on the cave roof, it isn't a level-appropriate challenge for the group, but it can still drop on someone and cost them a surge or two. It's still scary and exciting. Don't balance every fight all the time, and especially don't make every fight the ultimate "OMG we're gonna die" fight. It gets old and saps excitement from the fights that should actually be edge-of-your-seat scary. It also dominates the session too much because of the time involved in running level-appropriate fights.
• Lack of Exploration / Flavor
I covered this a bit above, but it's disappointing in 4E modules that there often is no description of empty rooms, or empty rooms at all. There aren't places that are cool, or interesting without somehow being tactical. In many of the modules, there isn't even much in the way of fun terrain to have your combats in. Just square rooms with unspecified statues. No mention of rugs, tapestries, slimy mold on the walls, dripping stalactites, or much of anything else. Look more kobolds in a square room. /yawn.
• Lack of Interesting Puzzles
I like puzzles and riddles. Where'd they go? They seem to be an iconic part of D&D that got left on the cutting room floor when 4E was being designed. That makes me sad. I realize there are some, such as one in Pyramid of Shadows with the keys, but the clues are kind of lame (First in hardness, not in place? - really?), and I took the great illustration associated with it (the three keys and keyholes with the sun, moon, and stars) rewrote all the clues, and recycled it for my current adventure. I will likewise be redesigning the trials in the minotaur proving grounds area for Thunderspire, to make a couple of them more about puzzle solving and less about combat.
• Organization Issues
Splitting info between books of the adventure can be somewhat annoying. It's hard to find descriptions of NPCs in any concise way; they are often split among locations, or in an encounter where you are questioning people. It's hard to find the info when you need it. I think Book 1 could be the main adventure, and book 2 could be the pretty illustrations to show players along with stats for monsters, and the maps.
• Not Knowing the BBEG's Plot or Motivation
The DM may know why Paldemar (Thunderspire) is doing whatever it is he's doing, but the players really never meet him or interact with him in any way. It's worse for Kalarel in Keep on the Shadowfell, who they have no way of learning about if you run the mod as written. Sure there's a lot of backstory, but no means of communicating it to the players. If I wanted to read a novel, I'd do that. I want information that matters when running the game, so writing backstory isn't enough. There has to be a way to get it into play or it doesn't count. Why would the characters care enough about these guys to be really satisfied when they finally slay the BBEG of the mod? As written, they don't.
• Dangling Plot Threads / Poor Story Development
So getting the mirror from the dragon burial site in Keep on the Shadowfell does what exactly? How does it matter in any way? Why is it even there if it doesn't make it easier to disrupt the ritual somehow? That kind of thing is a failure to make meaningful connections between elements of the story. You want to reward the players for being clever, for going the extra mile, and for using the plot devices that you handed to them in the first place. Here, there's no reason to because gee, that thing that seemed so important is utterly meaningless in the end. If you introduce some device in the story, don't forget about it later. Make it matter. The decisions the characters make in the course of the adventure likewise need to matter. There needs to be a reward for smart thinking, paying attention to the story, and clever planning using the knowledge you've gained. Fewer "Even if the group tries to negotiate, use a disguise, or a clever ruse, the bad guys figure it out and attack as soon as anyone comes in the room." meh. That's tedious.
Hopefully that's somewhat helpful. I'd like to see more room by room descriptions, tied to a numbered map. Describe the creatures there, but I'm thinking the delve format is causing more issues of page-flipping than it solves. Put the stat blocks in the other book, along with the maps. You have some great artists working for you, and many of the maps and illustrations of the major scenes of the dungeons are really well-drawn. Please don't always make your maps built solely with dungeon tiles; not all of us use them. (They don't come in hex!

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The current splitting of room descriptions between the delve format encounters and the general overview on another page, and lack of detail in those descriptions really discourages exploration and the feeling that some ground is being covered. If all you get done is two fights out of a huge module in the course of a 4 hour session it feels like no real progress is being made. All too often, that's what it's like.
I have to make up answers rather than replying "I have no idea" when players ask about stuff in the module. That's okay if they ask something really detailed or unusual, but "What's in the trunk?" shouldn't be that way. Treasure is another failure in many modules (at least the older ones I have the most experience with). There isn't much of it, and often it doesn't fit well with the parcel system. Newer mods may have fixed that somewhat.
To sum up (The TLDR version): Better skill challenges, better terrain, more terrain powers, more exploration, more puzzles, more accessible story (not just DM summary info), more easy fights, and make the tough ones really epic. Less combat, less grind.