Fallen Enchantress is very much its own game. It's strengths over its grandaddy of a game MoM are clearly:
Customization: the heroes, the leveling, the units, the equipment.
Technology: this one is self evident.
RPG elements: the quests and wildlands are fantastic new additions to the genre.
The A.I.: Although much maligned, it does seem to be improving, and is already better than that of MoM (barring some strange flukes that take place from time to time).
However the game remains, in my eyes at least, somewhat 'bland'. Its simple fantasy, not HIGH fantasy (despite the prevalence of magic and godlike beings). It doesn't feel epic enough. This is where MoM shines compared to FE. Its scope and ambition.
A lot has to do with the races: all are basically human.
So trogs are half orcs, Shades are half undead, amarians are half elves, etc. But the most recognizeable feature is still human. Where are the elves, the dwarves the draconians and the beastmen? Their absence is keenly felt. A huge step could be taken if each army had a STRONG contingent of unique troop bases to operate from, much like the Gilden have the iron golems and the troggs have juggerneuts. They should go all out, have iron golem troops, mithral paladins as bases on which the customization addons can then be applied. Same goes for troggs, give them human sized genetic throwbacks with all the fury less of the brain (orcs), give them runts are killed by exposure (like in most warrior cultures) but with the right enlightened social technology can be saved and turned into menial laborers and human shields (goblins) This would help distinguish the races, make them stand out more. As it is right now, I am basically selecting a template of skills and racial traits, not selecting a RACE.
The other important ingredient that I feel is missing: enough magic.
For a world as magically saturated as this one I always felt the spells are very limited. You need more magic selection.
At the same time you need more summoned creatures tied to each circle of magic. You need to see these creatures roaming in the world, tied to their elements and their settings. And you need the ability to summon more than just elementals of the appropiate circle.
You also need global spells. Give them a full screen casting animation, give them a visible effect on the world and these will be very rewarding spells to cast and see in play.
Combine this with item crafting (especially using the reagents your heroes keep on picking up) and add to this more monsters, more quests, more loot and you have a very rich magical setting that would set the game apart.
All this being said I can sum up as following: Keep developing FE, but look to MoM for inspiration to add some more grandeur and scope to the game.