All this goes with the disclaimer of "for my preferences" -- obviously, I am not your sole customer and, frankly, things that I like may well be disliked by the majority at large. But here is food for thought since you're asking
Consecutive Pages
I'll start with a favorite thing that WotC -is- doing well. The recent trend in layout has been to have all info for a given encounter on 2 page, or at least on consecutive pages for the longer ones. I don't like flipping to multiple books or an index. I love the fact that it is all right there with minimal flipping. I'd be sad if this format went away.
Shorter but more frequent descriptive text
The block of text for DMs to read aloud - After a sentence or two, players often zone out. But at the same time, they are great ways to fill in flavor and atmosphere. So perhaps keep them on the short side but possibly peppered in more often?
Plot Hook Variety:
For longer modules, I'd like to see more variety in plot hooks. This is a tricky one since you can not make a plot hook for the millions of self-evolving campaign worlds and PCs out there. But (generally speaking) the existing plot hooks often boil down to a) "the default: you answer a letter for help" b) "the friend who some PC knows from his past is in trouble and needs help" and c) "you hear of treasure/monster/dungeon of legend and want to see/tame/explore it for yourself"
And, yes, these make good stand by hooks. But sometimes it's hard to know how far you can stray from the given plot hooks to make it more personalized to your own campaign. I am not sure what to suggest here since potential plot hooks vary by plot, but my main point here is that some additional variety to help make it easier for a DM to personalize a plot hook to the party... and for these longer adventures, you want/need a stronger buy-in from the PCs rather than just because the player controlling the PC says so.
Nonlinear:
Linear adventures are easier to write, I get that. They are also easier for a DM to follow, I get that too. But when playing, the path sometimes feels very constricting to the point of making me (as a player) feel powerless in choice;'why bother making a decision, just follow the trail without pause" Yes, dungeons are often linear by architectural design. But when outside the dungeon, often is the case that the NPCs will just keep pointing you back to the linear path even if you wanted to try and do something different.
Location, Location, Location...
Every low level adventure seems to center around going in to ruins as the dungeon. I like ruin-style dungeons (they offer great places to stick in history and lore along the way), but I'd also like it if some more adventures that did not center around a ruin-based dungeon crawl (but above ground temples, castles, wilderness, taverns, etc that as the 'dungeon' is fine.. just something to offer variety!)
Interesting encounter features
Even if I don't use the encounter as scripted, there should be potential to take a great location or terrain feature for my own encounter. In general, this is something WotC adventures (that i've seen) often try to do, at least for the climactic encounters. And more often than not, WotC does this well.
Encounter Mix
I know this is somewhat of a silly thing to say since it is also in the DMG, but for newbie DMs, and for DMs that are not used to running modules, a small sidebar at the start that reminds DMs to consider changing the enemy mix if their party lacks some particular role. I.e. "If the party doesn't have many strikers, consider replacing 1 orc brute with 4 orc minions in encounters 2, 5, and 8. Or consider reducing John Doe's HP by 10 in encounter 13. Refer to the DMG for other ideas if the party lacks a particular role"
Obviously, this one just refers to your big adventure modules, it's not a practical suggestion for the short Dungeon Magazine adventures.
Fewer Combat Slogs
There have been some adventures where the pacing seems off, they seem to be combat after combat after combat. So some places to stick in NPC interaction and/or noncombat encounters, along with appropriate prompts to help DMs who are not used to doing NPC conversations.
player-ready visuals
These can be handouts or even just a page with a blank&white map or color illustration, but something that the players can see to give them a sense of mood/theme/etc. i mention this because sometimes when there is an image, or map that i would want to show to give a sense of what a corridor might look like or how the castle is so elaborately decorated, it often has DM-secrets showing on it too.
Story
A story that makes me as a player want to keep my PC invested (this goes partially with making good hooks, but also with how the story plays out).
Obviously, there is the struggle between space availability and necessity
You'll notice the general theme in several of my above suggestions are ways to increase feel/immersion for the players.
(I'm tired, so apologies for having scattered thoughts. I may think of more stuff later, but that's it from my sleep-deprived brain at the moment
)
PS. I would not kick yourselves too hard over your initial assertion. I do not think WotC is overall any better or worse than other publishers when it comes to modules. You have some that work out well in execution, and some that don't, just like everyone else. It's just that it is from you (WotC) that it gets the most attention, table-play, and scrutiny.
