I have read the whole topic, and let me just chip in about a few things I'd like to see fixed/improved - things I saw others mention, and a few ideas of my own:
1) "On the hero panel the "go top" button (when you have too many hero to show all in the same time and you can scroll down/up) is under the upper UI." - and why is the list of heroes arbitrarily capped? It would be nice if we could set the number of lines we want to have on the screen in the options. I hate not being able to see all of my heroes stats...
2) Some sorting options to hero panel. - ie sorting by class, level. -> yes, please. In particular: being able to sort them by party, action and HEALTH (dynamic)
3) Option to show heroes' name and level in the game like it was in the first game. - yes, please
4) Option to continue missions after winning and choosing the lord. -> YES, PLEASE
5) Fear flags should stay as long as the player remove them. -> yeah... I used a fear flag recently for the first time, and then it disappeared...why? (also: is there a point in putting gold into a fear flag?)
6) Monsters should loot the money from destroyed buildings as in the original game. - yes...
That's from the original posts. Stuff from other posters I liked:
* more heroes' personality (actions: patrolling the street, sleeping, falling in love, seeking revenge

)
* more heroes' interaction with buildings / more recreation buildings for heroes (gambling hall, food stalls, fountain to toss the gold in for good luck (and rogues could steal from), royal gardens with their rest and free spell, and finally: bring back the gazebo!

, etc.)
* more heroes' socializing - talking, quarreling, preaching...
* stress-o-meter requiring heroes to do some relaxation...
* planting and collecting plants for some classes was fun
* dead heroes should leave treasure behind, and/or it should be stolen by monsters
* heroes should not ignore monsters that are close to them if they are not fleeing
* high level heroes should take the initiative and raid lairs
* a hero in a party that is not a leader should still be marked (small star); also the stars could have a number in them indicating on the hero rooster which party they are in (and I'd like to be able to sort the rooster by party, with leader in the front, and members to the right...)
* why are rangers no longer gaining exp from exploring?
* where is the library?

It could be used for other classes then mages, it could be a counterpart for the training arena/fairground allowing heroes to raise some stats a little...
* monsters lairs should respawn after some time
* monsters spending money - upgrading the lairs sounds fun

* dungeon idea by maximusss and ValentineHeart is fun (would probably require its own expansion, but... why not?)
* monsters should try to run away if outmatched, some smart monsters shouldn't be suicidal...
* patrol flag - yes!
* trading posts offering goods
* flag should not only say how many are interested in it, but who
* better interface for spell casting on parties
* more indicators - for when resurrection from tombstone is viable, for when a spell with a duration expires...
* more upgrades for defensive buildings
* party formation improvement - dismiss heroes from the inn gathering if you don't want them in the party (so they wouldn't come back for a few minutes)
* fear flag for monsters - why not
* why the dwarves no longer build?
* healers should prioritize healing over everything else...
* building destruction notifications for things other then trade posts...
* heroes should not consume magic bazaar potions till they need them; how often do I see heroes safe in the middle of the town gulping them... also, they should not consume them for easy fights (15 level hero gulping potions to take down a sewer rat...). Note: this is post patch 1.3
* undead should be immune to poison, fire elementals should be immune to fire. etc.
* buying new stuff should be changed to more specific ("ex. buying new weapon")
My own ideas I haven't seen elsewhere here:
* destroyed den having some special (item) treasure?
* personality for heroes could be part of their description, assigned from a list of quirks
* rangers should hunt food animals

* somebody mentioned that tax collectors are not respawned beyond two - yet we are not even told when they die; is it possible to resurrect them?
* any chance for monks?
* more zoom in?
* blacksmith should bring in at least a little default income (50, 25, anything) - peasants buy tools too...
* "gather here" flag
* can the wizards towers be set on autorecharge?
* I am not sure - but are the rogues still able to steal money from other heroes & buildings & graveyard?
* monsters leveling up
* unique items found in lairs - flaming swords, magic armor, etc.
** and give them to lords to make them truly unique
*** why only one hall of lords? I want to have all of them in my campaign...
*it would be nice if all guilds sold something to other heroes; currently many don't
* max/min level for flags
* ranged attack classes should maintain range from enemy, use "fighting retreat", etc.
Things that may already be implemented? I am not sure...
* monsters forming their own parties (some of course more likely then others... wolf packs, vampires and leaches controlling lesser undead, etc.)
* treasure chests containing non-gold items (since some of my heroes get items I know I am not selling yet I presume this happens... but a notification about heroes finding special treasures would be nice)
* are flags split evenly between nearby heroes?
* what, wizards no longer have area spells?
Final thought: more sim, please. I hate most RTSes, I loved the old Majesty. It is a niche sim-RTS - don't lose the sim part, there is plenty of RTS that will compete you out of the market... Majesty's strength was the sim part.
If there are some balance issues, as some suggested, why not add a SIM switch? If you switch it on, the heroes do more misc stuff but also have more initiative on the map, recreating the old feel.