I think a lot of fans out there know what is a good 4x strategy game.
However, games that sold millions of copy bring new concepts to the genre. I.E Total ware series, turn base strategy, real time tactics.
Something that have been overlooked in the past about fantasy strategy based, is the progression and evolution of the unit.
The unit don't have a lot to offer in RPG terms for all those war games before.
The most we have seen in the unit progression, is UPGRADE in HOMM or UNIT XP level in Total war.
Tactical RPG game offer a wide variety of upgrade for the unit. (Ogre Battle, Final fantasy tactics) The upgrade path, with the appropriate XP and/or event and/or group composition and/or heroes affinities and/or physical place (tower of the dark could upgrade a swordman elite in a wraith swordman, if 5000 xp and a summon wraith spells by a black mage)...
A deep system for upgrading unit, with many steps to upgrade them.... like having a Lich Lord should be not tedious, but suffiently difficult to don't have 5000 Lich Lord and 2 swordman in an army.
But, i cannot stress more it, UNIT progression should be the main new feature develop with care and a lot of combinaison to do... like, it is my 4th game, 3 months after the first... and it's the first time I can upgrade those wraith swordman in wraith knight.
The advocate of anti-micromanagement will say NO... I say to them, don't micro it, and you will be happy. But let people that want upgrade unit, take the time and effort and knowledge to do it. Not simply like HOMM : click on the building upgrade -> upgrade your troops.
Having Vampire Lord is a nice addition from the Vampire unit of course. It is fast, easy and straigthforward.. GOOD! But those Vampire Lord unit will be the same all the game long... to change them, you will change your hero or recruit more vampire.
So, after 2 games playing with Vampire Lord, I am a bit bored of them... no way to change them, to specialized them, to do something real nice... Like a Vampire Mage for example... or a Vampire Thief (stealth and backstab)...
The Unit system could use a CLASS system. That class can be changed and/or evolve with XP point.
And I want more, I want UNIT GEAR has well...

Gear that you create at your city.
Gear that you find in dungeon.
Gear that you find on the battlefield's corpses.
And like someone said, the evolving unit class system could use some requirement with gear to evolve. Like a skeleton swordman, equip with a full plate and a horse could be a skeleton knight.
Gear is level dependant in most case, so your units should be really class evolve to use magical items and so on.
Surely, that kind of feature would need some AI option for the players, to remove the tedious aspect of it. You can put some config to the AI (artificial intelligence... not sure if I don't mix with IA in french though) like the gambit in final fantasy XII where you give priorities of gear and conditions to do gears.
Like:
1- Horse production = 20% unit (this will produce horse gears for unit in a proportion of 20% of your total unit number)
2- Sword production = 15%
3- Full plate = 20%
So, the first condition (Horses) will prevail the two others. The kingdom have put priorities on horses.
Then, you could have an auto-equip feature if armies come in (option/on/off - > with AI custom priorities) to reduced the tedium (the concept of some lazy people) of managing gears of Armies.
I played Master of Magic for 1 year. I think it is the fantasy 4x I played the most. I replayed a lot of games later until I got windows XP. But even that microprose game (the only company should I pray for them to continu to offer more to the gaming sphere at that time, because they had give a lot more than Sierra or EA) was not enough in the massiveness of unit choice, versus conquering.
Dominion 3 - is something you must play to see what a 4x made in a basement can be. It is so popular actually, even with low grade graphics, that you cannot miss it. And in that regard, Dominion miss a lot of deepness in the city managing department, the unit system of independant troops versus nationnal troops is interesting. The magical system is really interesting, the unit can channel some spells of your knowledge with point in the magic school. Forged items permit your mage to have boost in spell school to use that lvl 3 fireball you had research, like having a ring of wizardry. Something power gamer loved to do in HOMM, is raising all the last unit level of each race castle they have to make an armies of Dragons/Behemot/Devils/Angels...
In that regard, that unit evolving system can bring a knight to become a Dragon Knight (merge of two units, to have better skills) or a Dragon Mage ( spellcasting on the back of a dragon ).
I can't stress more :
Evolving UNIT - Class and GEAR -> Infinite possibilities -> replay value boosted
The gear aspect of it, is easily a winner and you had experienced it with Gal CIV custom ships and TECH research.
CLass unit have been done in Tactical RPG game (that are really boring if you don't like the concept of class unit evolving because it is the only RPG concept in play for that king of game that sold hundreds thousands of copies).
The merger should give the old school tabletop wargame the real feeling back again.
In that regard, the 4x fan will play their gameplay like before, but you will take new peoples in the genre, because you will bring new concepts and deepness in it. That will raise the bar of the future fantasy 4x and surely put your title in the classic game like MoM.
Arkanciel