Here my suggestions. I think this game is fun and decent out of the box (barring those stability issues some people are having), but there's still a lot of work to do before it's a great game and a classic of the genre. I'm still pretty optimistic and think it'll get there eventually. I can certainly see all the potential this new engine has to take us there.
What I think need to be priorities:
1) AI AI AI. I like that there are diplomatic and peaceful options, but the AI needs to put SOME pressure on the player, especially those supposedly evil empires? Right now in every game I've played the AI has basically left me alone until I'm ready to conquer them or win through one of the other paths.
2) Tech trees. There need to be a lot more techs, like 5x more would be good. The trees all feel very light and unbalanced. By the time I've gotten 4-5 good cities set up, have built up a decent army and am ready to go on the warpath (i.e. it feels like mid-game) I've already researched most of the technologies I need. Some of this is pacing too, techs should maybe cost a bit more to research to drag things out more, or tone down the bonus those libraries give + their multipliers. But I'd much prefer to just have more techs and more meaningful tech choices. Need to give players more reasons to specialize rather than just jumping from one tree to the next since you run out of techs so quickly.
3) Champions all feel bland and undifferentiated. Special abilities as part of leveling them are the key to solving this I think. My assasin character can level in first strike and poison abilities, my mage gets a mana regen ability, my fighter gets an army morale boost ability or a cleave ability etc etc. Room for some of these abilities to be unlocked by techs to tie the two together better. Also there need to be equipment restrictions and more reasons to equip different heroes different ways. Right now I'm equiping everyone in the most expensive armor and sword and shield as soon as I can afford it (including my channelers, outfitting Procipinee in full plate with a shield and broadsword is pretty ludicrous but I have no better options).
Basically they need to think about classes of heroes like an rpg rather than generic stat based leveling. Stats should level automatically based on class, equipment should be restricted by class (no mages in plate mail thanks!) and the choice the player should get to make on leveling should be which abilities they get, which is much more interesting.
4) Cities. This is actually I think the most solid part of the game right now, but there needs to be more reasons to specialize cities rather than just building every building in most cases. Also better differentiation between empire and kingdom cities as well as solving the issues when you conquer a city of the other type and then get to build all the generic buildings twice (i.e you end up with both the empire and kingdom version of the building if you want). Also balance resources better along with all their multiplier buildings, I am rarely struggling for food or gold once my first few cities are settled unless I get a really bad start location and am boxed in.
5) Magic. I think there need to be less spells, there are far too many right now. The issue is that the vast majority don't feel like they are worth casting, especially since it's going to take many turns for spent mana to regen. The only spells I really find worth using are a few direct damage, the occasional summon, and teleport. They need to make each and every spell more interesting and actually worth casting. Needs to be lots more linking in this area to the tech tree, currently it's only 3 techs to unlock all the spells in the game. More interesting choices needed.
6) More differentiation between all the different factions. They all basically play the same currently. They need to have distinct abilities, advantages and weaknesses, units and buildings, as well as their own unique spellbooks.