Here is what I think of the game in its current version. First I must say that I really enjoy this game, and am looking forward to what is to come.
What FE does better than most games already (the great stuff)
1. All units gets experience, even the wildlings. Fantastic. This is something that can be used in interesting ways in the future as well. Imagine a roaming strong monster getting stronger and stronger as it chews up the wild 
2. When you change gear on a unit its apperance actually change. A nice little touch there
3. Resources are produced per turn and require long term planning. Late game you might need 140 metal to produce your tough defender forces. Lets hope you thought of this earlier in the game when those outposts were planned
Other resources like material and food determine production and population. Me likes!
4. We can get spells from research, level ups and through other means. This is a great start, and I hope it will be expanded upon.
5. We can hire monsters like Drakes (they are insane with their Sweep ability, is the damage calc bugged?).
6. There are lots of weapons with interesting effects. Give us more
7. The monsters have AI. This should be improved upon to give more personalities to the monsters. Some (spiders?) could eventually group if they are not killed early game. Thus making more interesting opponents. Some should hunt you down the moment they see you. Some should be cowards and try to flee. Some could hate Kingdom/Empire and almost exclusively attack one faction.
What is still a bit thin (what I want to be improved the most)
1. City building is still a bit shallow. Has been discussed a lot. I want buildings that does special stuff. Tower of corruption, available only for Empire (+0.5 growth , all Kingdom players get -0.2 growth). Library of lore (gives access to a unique spell, only one can be built in the world). Travellers inn (at random intervals some travelling unit will offer to go into your service for a cost)+++
2. Better quests. I want a witch to tell me to focus on air shards to promote her religion. If I get 4 air shards she will give me two air elementals. I want a man seeking revenge for his lost family and rewarding me with 100 mana for each troll I kill for the rest of the game. 
3. The AI of the monsters seem to treat AI players and human players differently. I often see AI units passing monsters without being attacked. On the other hand I see that the AI sovereigns have lots of wounds. Is that from warring or bad estimats of what monsters they should attack?
4. The AI cannot build tough enough armies to challenge the humans (yet). They need to try to make a few elite armies. Start by picking up the free stuff in the world 
5. More variance in the tech research. We need more options. I would like techs that exculde eachother and other goodies. If I commit to the lord of fire and research fire shield tech (gives a few fire spells) then the lord of wind will not grant me access to the tech air travel. You get the picture
6. Mercenaries. I would like to hire special mercenaries that are not otherwise available in the game. Some units with special abilities that are cooler than normal units. Units that I want to protect and use at the same time. They could be attracted by some special building, completing quests and such.
7. Monster control. I would like to bribe/control monsters in an indirect way. Umber should be able to pay a troll to go and attack a certain faction in general, without actually controlling the unit. That would be awesome. I would also like to see what this units see (so that the rampage is not in my fog of war).
8. Faction variation. Discussed to death already.
9. More passive abilities. Take a look at Kings Bounty and all the abilities that the units have there. I would like passive abilities like Horseslayer (+5 attack against all units on horse), Aggressor (+2 attack in all battles outside your area), Souldrinker (+3 hitpoints on each successful attack the unit does), Woodsman(+2 attack and defense in wood areas) +++
10. Random events. I would like some cool random events that could really change the game (make an option to turn this off for the pureblood who dont like surprises). Events could be: Storm from the east: Due to heavy battles in a far away land, fleeing forces has landed on our shores and are looking for land to live in (lots of monsters arriving at the edge of the map). Bad Harvest: No population growth in the world for 10 rounds. Troll shaman. A regular troll has discovered the book of blood and turned into a very strong Troll Shaman. He is attracting trolls and making a huge dangerous army.
These are my main points at the moment.