First I would like to start out with how IMPRESSED I am with Fallen Enchantress.
It is much better than E:WoM.
It looks prettier, battles are more fun, champions are more fun (and leveling champions are more fun).
I like the Spell skills (death 1-6, etc)
I like how imbued champions cannot automatically cast all spells
I think I agree with Derek that the 'imbue' spell is not needed. Though I really love the concept of the 'Paragon' spell 
I like how Sovereigns don't get 'injuries' but Champions do. Makes the Sov a bit special.
-> I really like quests that have multiple battles in a row.
-> I really like the diversity in weapon stats, I think this could be expanded and improved upon.
-> I REALLY like how HP increases with level 
-> I like the 'Serpent's Pact' Civ trait (makes Drake recruitment unique, instead of something anyone can do)
what has stayed the same:
I haven't done any of the higher level quests yet, but the beginning quests are about on Par with E:WoM
Concerns
-> I don't like how, in a unit, either they all hit or they all miss. individual figures should be able to hit or miss individually.
-> Non-Mounted units having more than 3 tactical move (charge is kind of silly, and 10 move guys are really silly ... you already can get enough initiative to move TWICE before anyone else ... why isn't that enough?
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Comments:
Honestly I don't mind Discipline (+1 str per level) ... I think it'd be balanced if units couldn't move 6-8 tiles in the first turn .. (charge anyone?)
On that note, I think 'Charge' is a bit silly. Maybe it could be an activated skill on mounted units ... OR changed to +1 movement and may be activated every 3 turns or so. (perhaps at a temporary loss of Dexterity?) +1 move, +3 attack, -2 dex.
-> I think it would be more interesting if Assassin type weapons (Daggers + Bows) had dexterity bonuses.
ie: Bows have a dexterity bonus similar to strength ... Daggers have a 1/3 strength bonus and 2/3 dexterity bonus.
-> I think Path's should be mutualy exclusive, or at least a 2 path minimum (is there already a 2 path minimum? haven't gotten 3 yet)
-> I also don't get why 'SPEARS' are the weapon which ignores a percentage of armor value. Why isn't it hammers/maces/mauls?
-> I like some of the abilities, are some abilities only supposed to be good at low levels though?
-> regular troops should probably have a max level
-> Champions + Sovereigns should never have a max level
-> I think Champs should be able to attach and detach from units
-> maybe its b/c I only started with 1 champion ... but I didn't see champions being overpowered early on. The only one that is (deservingly) op is my deadly Soveriegn 
-> That being said, it IS rediculous that he can cross the map in LESS THAN ONE ROUND. In fact, he can move at least 10 tiles in the first turn of combat ... I think things like 'quick' should only increase Dex, Initiative, and Dodge.
-> I think I'll make a new post on the relationship between Strength and Movement
-> I think Intelligence should also DECREASE mana costs for spells (somewhat)
-> While brute and finesse are nice ... I think there should be equivalent traits that buff you vs STRONGER enemies (like heroism, daring, beast slayer, hero slayer?, etc)
Bugs
-> 'sure strike' didn't show up as a potential ability on one of my Champions. Didn't pick the trait after that.
-> I think Champions that 'die' and get an injury should spawn in the capital/nearest city ... instead of remaining in the stack to potentially get killed again for a second injury (multiple battle quests). (champion in question was in my Sov's stack).