These are minor suggestions that I think would make many people happy, yet not take enormous amounts of developer time. Mostly they are aimed at clearing up the nonstandard flagging/quest advancement issues that some quests have.
1) Changes to flagging - Necropolis Crypts
We've heard already that you are fixing the mess that is VON flagging. Can I suggest that you make similar changes to the Bloody Crypt, Shadow Crypt and (to a lesser extent) the Cursed Crypt.
These should all be flag once and be permaflagged (which the Cursed Crypt partially is and the other two are not). Secondly, the quest givers should only require that you have done the precursor quests once ever, rather than requiring you to have completed them and also to have not reacquired the quests. (The Mindsunder has this coding - the quest giver will speak to you if and only if you have completed I Dream of Jeets, but you can enter the quest regardless if you have an opener.
In addition to making the Crypt quests more popular (which they should be, all three are pretty well-made quests), this would make running the prequests less painful. I made the mistake of opening elite Tomb of the Tormented for someone on my Sorc once - to reflag for the Cursed Crypt, I then had to rerun all four of those quests. Whoops!
2) Changes to flagging - I Dream of Jeets
Currently there is no way to enter I Dream of Jeets without having first completed Finding the Path, regardless of whether your other party members are on the quest. However, you can enter The Mindsunder without doing either, despite it being the end quest of the chain. This frustrates groups that run Finding the Path then have a person drop before I Dream of Jeets - it's harder to replace that person.
Both I Dream of Jeets and The Mindsunder should allow anyone to enter, as long as one person is currently 'on the quest'.
3) Changes to quest sequencing - Threnal
Here, I recommend reworking the end reward system and quest sequencing altogether.
I'd make it work like this - you have one quest giver that gives the East chain, and upon completion gives you a House Kundarak Badge of Commendation as well as a standard level 10 end reward. Another gives you the West chain, and on completion, a House Deneith Badge of Commendation and a level 11 end reward. A third quest giver will not speak to you unless you have completed both West and East - after you meet that requirement, he offers the South chain, and upon completion, he gives you a level 11 reward and a 'Traitor's Head' (which has flavor text indicating that it used to belong to our friend Coyle). These items are all bound-to-account collectibles.
Finally, a new NPC will take one of each Badge of Commendation plus the Head and give you a standard Threnal full chain end reward, you can repeat this quest as many times as you wish.
This would make running Threnal more popular - in particular the South wing. It is presently extremely difficult to find a group that will stay together for all of Threnal; it's also extremely difficult to find an elite opener.
4) Changes to quest sequencing - Delara's Tomb
Here I'd totally change the chain mechanics to be granted by Derek (as it is now), then to have players talk to Colaam once after each quest. Here's how I'd make it work.
Step 1: Speak to Derek. He directs you to speak to Colaam for further work.
Step 2: Speak to Colaam. He grants quest 1 - 'The Mystery of Delara's Tomb'.
Step 3: Defeat quest 1. Speak to Colaam, he grants quest 2 - 'The Missing Party' - and gives you the -1 ugly stick of greater idiot affinity.
Step 4: Defeat quest 2. Speak to Colaam, he grants quest 3, can't remember its name.
Step 5: Defeat quest 3. Speak to Colaam, he tells you that although you have stopped Delara, she will just be turned back into a wraith unless you slay the necromancer that is animating her. Colaam offers a level 7 end reward, then directs you to speak to Hargo Grimmare, and to get the truth out of him by whatever means are necessary.
Step 6: Speak to Hargo. He tells you about the dark side of Delara, and tells you that he stole her journal, and that it indicated she was being tormented by a necromancer Dreadlord Giddeon. He also tells you that he has found Giddeon's lair and bestows quest 4.
Step 7: Defeat quest 7. Speak to Colaam, he grants an end reward for the entire chain.
There - easier to get right, and no need to keep reminding parties 'talk to Colam, then Derek, then bluff/bribe Hargo, then talk to Delara, then Hargo' - just something straightforward that keeps the storyline intact but stops groups falling apart because the cleric didn't advance properly and refuses to continue unless the group repeats a part, but two party members haven't got time to do that.
5) Changes to flagging - Stealer of Souls
This should also be 'flag once and forget'. The reflagging is irritating, to say the least, even now that it's not as bad as it used to be. It's particularly frustrating to wait a long time for a cleric/FvS that is flagged, has some incentive to run SoS and is in the mood to - quite often SoS LFMs go up, fail to fill for 20 minutes, then fall apart. Were ti flag and forget, this would not be so bad - and were there rewards in there for people that aren't chasing a new DT sovereign rune, it'd be better still.
While you are at it, add Reaver's Refuge (requires you to have been there once) to Greater Teleport, and also the inside of the Twelve (for quick transportation to Amrath).