I bought the game back when it was in beta. Played a handful of times but never really got anywhere because it really wasn't very fun.
Played the FE beta once (maybe I'll give it another whirl this weekend). Definitely much improved, but still very confusing and awkward with too many systems within the game.
For example, equipment, particularly hero equipment. It's a pain to try and manage several inventories and trading items between characters takes a couple of extra steps. Units can also be equipped with particular armor and weapons. And when I say armor, I mean 7 different slots of armor (not to mention accessories)! Personally, I find detailed equipment systems in grand strategy games to be more of a burden than anything and I would dump it entirely. Or at the very least, axe about 80% of the options. I really don't want to worry about whether or not all of my spearmen have gloves or whether that staff for sale is 2% better than the one my mage currently has equipped.
Then there are just some strange design decisions. For instance, every time you create a building in a town, you have to decide where in the town's area of influence you want to place it. "Cool!" you might think, but it's not really. Building placement has zero effect on gameplay, so it's purely cosmetic. But usually I'm zoomed out to get a better overview, in which case the visual layout of each city is irrelevant and not overly noticeable. So what initially seems like a neat feature is actually just fluff that requires micromanagement. And it gets old pretty quickly.
The spell system is probably still to complex. Or maybe it's just that they throw too much at you to start. I played a warrior-type leader and I still have over a dozen available spells to cast from turn 1!
Citys and heroes gain levels, allowing you to given them new 'promotions' so to speak. Units also gain levels, but you get no input on how to make them better. There's just some inherent bonuses for being a higher level. So I find that kind of strange that I can customize my unit's equipment down to their underwear, but I cant customize their growth. You can customize units with special abilities and traits when you design them, but if you just want a couple of specialized troops, you have to make specific designs for each. You cant just build a warrior and then customize it as they gain experience.
Just a few annoyances off the top of my head. I still much prefer Civ. Civ4 did an excellent job of simplifying things while still keeping the game strategic and interesting. FE/WoM takes the opposite tact. In my current saved game I have a mana pool, a horse pool, a warg pool, a metal pool, shard pools (one for fire, one for air, one for and life), a diplomacy pool, a crystal pool, and probably more that I haven't yet discovered! Civ4 boiled this down to "do you have access to that material", which though seems overly simple at first glance, actually streamlines gameplay and makes it much more enjoyable, IMO.
Edit: And there seems to be no way to get updates/patches from within the game itself.