I haven't played too much, but these are my main concerns about the game:
1) Lack of diversity:
Everything feels the same. I do not find myself trying new things, because either I have no reason (see below) or because it's not different.
The one main difference between games are if your sovereign is a caster or a melee. Caster is for endgame where you can throw mana around, melee is for early game. Beyond choosing that, I play my race and tech tree the same way, pretty much ignoring the traits I picked for my race (I play custom usually) etc.
I wish for something more like MoM (insecticide patched) where I have a dozen of options to try to beat the game when it's on 'impossible' difficulty. The patched game is extremely hard, and you have to use a 'broken' build to beat it. Some builds are too slow, while others are not powerful enough. I have found 4 builds that managed to win it, and there are probably more.
Fallen Enchantress (and most other games when I compare them to MoM and MoO2, including the civs), as it is now, is really bland compared to a game from 95- we don't have as many spells, the races are nearly the same and there is not nearly as much versatility.
2) Lack of AI:
If I play the game on high difficulty, I simply reach a point where the computer sends wave after wave of magicians till I'm down. Due to the very low rate of experience heroes get from destroying armies, it means that he overwhelms me at some point.
If I play on "normal" difficulty, I am simply cleaning my zones till I feel bored, build a stack of doom and start destroying the AI till I feel that "GG I won" and go away.
The second option happens because I expanded a lot faster than the AI, cleaned the zone faster and got my hero to a higher level (which in turn means I can do this all over again and snowball).
note- I feel about the same option regarding civ4, civ5 and AoW3.
3) Game progression:
You start with a city, research techs and expand. All is fun and well, but the techs are boring. Researching better weapons just means that "yay my units grew stronger", in a very linear way. There is no real thought into it.
I expected at least a tradeoff that was supposed to be in the old Elemental that "I got this new shiny armor, but it weighs so much I have to give up on my giant sword. What to do?", or "Do I have 10 turns to build this unit, or should I build a few weaker ones?". The first is not an issue anymore beside choosing the weapon, and the second has one answer- yes. That is because the units in the game come in tiers. Units in different tiers can't do anything to units in higher tier, due to a much higher defense, much higher offense and a lot more health.
In civ and AoW, deciding to take 3 bad units for the price of 1 big unit could be a serious decision, if I actually believed that they will be able to kill it and survive in some form (in civ many of them will die, in aow a few will die, in mom a few might die depending on the gap in power). I do not find I believe in this kind of tactic in FE due to cost of the death of units, amount of units it's possible to bring to battle, and the gap in power.