Just weighing in as a FE and FFH2 (Civ4) customer who actually completed several games of each (probably not on hard setting

):
FE comments:
1. I like the hero emphasis (leveling, perk choices, item management) in FE generally, because the alternative would be a purely fantasy re-skinning of Turn based 4X, a la Civ4/Civ5, which would be a marketing failure in my opinion (case of being an also ran when a giant has already bagged and tagged the target audience). I agree there's room to tweak the hero/henchman power relative to the units power (hero-henchmen armies with XP-leveling perks seem a bit overpowered), which is probably going to come out of making more option levels for regular units' size/ower and making those available earlier with tech focus.
2. The fantasy turn-based genre is obviously really diverse in game play. I'm sure the WoM boards are full of discussions of it. There's MoM, HoMM, tactics RPGs, etc.. Having one engine being capable of tackling all of that is pretty sharp in my opinion. But obviously the default version of the game would have some focus problems trying to hit all the sub-genres. But there's lots of DLC opportunities if the game engine is done right and has good word of mouth, with DLC that hits all tastes (4X TB, role-player, tactics player). Just saying. I don't feel that FE is really failing if it is not MoM X. There's a lot of audience variety to target in the macro-genre of fantasy turn-based. Much more so than the sci-fi, Masters of Orions mold.
3. I like the attempts at role-player story-telling in FE: unique quests attached with unique locations, random fetch-quests, simple quest-line as an optional victory path. The multiple victory options go beyond straight 4X, and also agree with 4X trend of more than just conquest victories. FE has a good balance of victory options in my opinion, and easily check-marked for a competitive PvP match if there was one. The only negative is that the story telling is still pretty shallow overall, but that is moddable. Branching story-quests (Choose Your Own Adventure on the 4X turn-based tile world), maybe?
4. I like the perk-leveling in FE, which is what passes for computer RPGing these days (thanks Fallout/D&D3.x). It adds to the RPG feel. One weakness of it is perhaps out of control leveling through XP-leveling perks (e.g. semi-logarithmic growth). This is the main way henchmen/heroes break the game in that a unit with one hero backed by mostly henchman with training XP perks will quickly level themselves to a steam-roller victory, just by playing them on random exploration and popping enemy attacks.
This is definitely curbed by injuries, and unit farming has to be careful, but a proper henchman design can give them a head start to the XP-perks. I don't feel this is an insta-win but feels like it has that potential to break the game. It definitely makes Champions stand out as an odd-man, only of value if there aren't henchmen recruiting options.
5. The design your own unit stchick is a pretty powerful attraction for a gamer. I know WoM was semi-influenced by the power Spore had in that dept, even in being an overall failure at being a game (referencing Spore). MoM and Alpha Centauri both had the design your own unit thing going on very well in one way or the other (MoM by the on-the-fly unit spells and race-unit options). I wouldn't write it out. I know it was a powerful part of my enjoying Gal Civ I and II, and the other 4X space games. The lack of unit design (excepting the capital ships and tech research) made me less interested in replaying Sins of a Solar. I'd say FE has just enough unit design options thanks to spells and the tech tree, but there's just enough lack of variability in models and unit design that it's noticeable. Or lets say that the hero-henchman get the bulk of the unit variability because of the unique quest items. But overall there's some negative replayablity in FE just because the variability is still pretty limited and not new/interesting after about half-dozen to dozen play-throughs.
Overall, I'd say doing away with design-your-own-units would kind of be laughing in the face of pretty successful trend in 4X turn-based games (Civ4, Alpha Centauri, and nuances in several Civ-clones). It also tend to scream cynical DLC ploy to the cynical PC gamer. Prime examples: the Total War series DLC unit, which is pretty much only forgivable during the Steam sales when they're on 75%-off sale.
6. The tactical combat is a little weak in FE, but its still pretty well thought out (i.e. kind of a good tease, but could use more). The initiative, spell casting length, and counter-spelling was pretty fresh in my opinion and made the inclusion of battle winning spells balanceable (e.g. the neutral creep AIs being able to cast insta-kill vampyric Despairs, but that could be countered by a combination of charging with super-heroes and counterspelling). The options of choosing between avoiding target defenses, counterattacks, extra attacks, extra dodging etc is pretty well thought out ("interesting choices", no absolute steam roller omnipotent choice). There's a decent amount of tactical options from strategic options, which is good game design present in FE, imho. I'd just think there could be more of this (e.g. flying (terrain effect negation), more nuances in combat effects. This strategic choices influencing tactical micro-options and ultimately battles and the game is maybe a bane of the AI programmer, but what made MoM special, imho. More in balanced moderation would be good for future FE DLC, I think.
Along Brad's complaint about terrain, I'd say add tactical map terrain effects. All terrain effects currently are all or nothing (block movement to create channels) which isn't bad but even simple tactical tabletop battles (e.g. Hordes of the Things) have rules for terrain slowing, terrain providing cover/damage resistance. Age of Wonders and MoM had functional terrain defense when defending bona fide castles (walls/gates had to be besieged/flown over and siege units were significant). These are noticeably missing in FE tactical, such that I only manage tactical battles to ensure the battle has reached a turning point after an opening combo.
Terrain definitely influences strategy though. Box canyons, walls, channels, limited city sites (infertile/impassable zones) make FE definitely play like an original TB game and not a Civilization-clone. And the world features idea was a great implementation in FE to make terrain be part of the setting, questable, and reward even with new cities/city sites. That is good game design in FE imho.
My last 2-cents:
If there's one mod/DLC I'd like to see for FE, it'd be "King of Dragon Pass" (1999 game based on Glorantha setting, available on GOG). Call me weird, but that's a great combination of RPG fantasy setting, story-telling, and turn-based civ strategy (although more like Hammurabi than 4X turn-based). I'd actually like a scenario mod that emphasized agrarian economy (herd size) and de-emphasized the Civilization model of spamming and log-growth management of city growth. This definitely tackles the "one city challenge" is a different, interesting way. Elements of this should be in 4X games, imho.