I think the biggest thing for me is the blandness (lack of variation) in the world. Right now there are only a handfull of maps- I haven't played enough games to have them memorized but random map generation would help with making exloring interesting again. The random events and special locations should help with this. The wandering npcs dont seem to do much of anything unless confronted or when they decide to raid your town. Some kind of hierarchy or something so they interact with other things on the map would help, such as can raid/destroy map features, or fight eachother if they dont get allong.
Some kind of event/location procedural generation wouldnt be remiss either (ie creating a goodie hut following rules or a formula and getting the specifics elements of it chosen from tables for each part). A simple example would be terrain(swamp,hills)-tile(goodie hut graphic)-reward(treasure, combat, lore,etc). Could have it do a roll when placing goodie huts to determine first if it would pull from a pre-gen list (how they are now), or create a random one.
I also agree on the faction/race differences not doing as much as they could to change play style (or feel/seem different at least). I imagine its a difficult balance between making them different and not forceing a given style on you. Not really sure how to spice it up though. Perhaps some kind of lore/history tie in with your structures/build style or the improvement tree (perhaps additional improvement levels to prefered buildings, unique units, or better improvement performance (or non related bonus) from prefered structures). Even something like HF did with the expanded factions (primarily the unique structure tiles to a faction for base buildings) help. Hopefully the custom faction tech tree thing will be implemented differently (as it seems like it might with the change to how techs look to work) so a full tech tree doesnt have to be copied/created as it does currently with the elves. Or at least a frame reference tree/ style to choose from (ie kingdom tarth, empire trog, etc) to emulate off of with hooks or something so you could just substitute/ change the required entries without having to copy stuff that wouldn't be different. Heavenfall would be able to provide better input on that.
The tactical combat is pretty crap though (functional but pretty bare bones). I usually just sim it. Its about as tactical as checkers (or a bit better) Some obstructions, or value to terrain tiles in the tac combat would help probably even more than improvements to the AI other than to recognize the value of positioning on terrain.
Disgaea had lots of variation in strike zones and attacks that could change the position of targets and attacker alike. Some of that would help or putting some value in unit facing (ie hitting from the back or sides of a unit ) or position in relation to other units (adjacent- which could be handled by aura type abilities). Say for example the unit gets a bonus to defense and vs. knockdown when flanked by friendly units, and a bonus vs. knockback when a friendly unit is behind them. It would probably work best to tie these into abilities that could be put onto a unit at creation (or as a bonus from equipment). There could be a compatible training bonus where the bonus applies when adjacent friendly units are fielding the same piece of equipment or ability.
The overkill ability mentioned in the dev journal sounds like it would help some with this issue or at least is kind of in the same vein. Having different abilities or features available to the units would help to differentiate them from eachother, and customization to have more purpose.- you could even work it similar to gal civ2 where the armor and weapons would work like the bling pieces that are just for show (or set what abilities are available to the unit based on the type/class of the equipment added), and abilities are what make the larger impact in unit performance. For example the weapon could determine the type of damage done, and armor the type resisted. Magical parts could add bonuses or additional types and/or abilities. Have the abilities make the stat alterations to the unit and effect training time, and cost (the same way armor and such do now). Then new abilities or unit features can be added/implemented more easily than thrue the creation of new equipment.
Lets say for example that a dagger and short sword both allow slashing type damage. So you could equip your peasent with either and have them do slashing damage. Then you could choose how much training they will have with that weapon class (slash), +0, +1, etc. with each costing more resources than the last to have trained into them. Alternatively it could be generic ranks in weapon proficency. It could keep equipment from becoming obsolete. Lets say that the difference between the two items is either anouther ability (like better crit damage, better crit%, +1 max damage, etc) or +1 rank in slashing applied by the short sword. Im sure there are a few things Im not thinking of that would be problems with this type of system (such as making weapons/armor changes a bit less impactfull or direct in how they work), but maybee the idea will help.