Fallen Enchantress is a fun game, but I feel like it lost too much "character" when it was overhauled from WoM. In particular, I really miss the big maps, ships, and dynasties. They made the world feel more alive and real. Here's a few favorites:
Population mattered during wars
Deciding how many units to build in a city for my army was a real factor, your population was reduced and wars actually devastated your people. They couldn't go on for very long until you simply ran out of people to fight with. I love games that factor population into army size.
Sea travel
In WoM you could set sail, find lost islands and back door routes to defeat your enemies with. Fantasy isn't complete without being able to take to the seas. I didn't care that the AI couldn't use it, that I could was good enough.
Dynasties
This is a big one. In my opinion, an entire dimension of the game was removed when Dynasties were taken out. Champions in WoM were far more than just chess pieces to boost your army with - they had lives of their own, they were born and died, married and had children. Losing a spouse in a battle was a big deal and the game told a story through these family lines. Marrying off a family member to another faction was awesome and reminded me of A Song of Ice and Fire.
Large Maps
Maps in WoM were enormous, they would last you months and months of play time. You really felt like you were traveling over a giant continent. In FE, I feel like it's more of an RTS with turns, and small "skirmish" maps, not epic worlds to explore.
Permadeath
Heroes in WoM could die. Death meant something. In FE, losing a fight just means getting a cheesy scar condition.
Interesting/Strategic cities
In WoM, cities could be planned and arranged to look just how you wanted it, and they could also be used as strategic choke points wherever you wanted on the map. They could be placed so enemies could not move past them without fighting, and they didn't need silly designated areas to be built.
Multiplayer
Yes, multiplayer in WoM wasn't the greatest, but it was there and it was fun.
Fallen Enchantress is a tighter, more focused game. But we lost quite a bit of the theme from WoM that made things interesting. Some may argue that if it doesn't have a real, quantifiable effect on the game, then we don't need it. I disagree. The intangibles give a game character, like Dynasties and Ships. WoM was both a kingdom simulator and a war game, but I feel like FE is just a war game. A lot of things have been dumbed down from WoM, there is less customization and a little too much "default" going on.
If we could see just half of the things above re-implemented in Fallen enchantress, I think I'd be far happier with it. Here's hoping that Stardock changes focus a little bit now that FE has been released. The game balance and focus has been done well, now we need some more of the goodies put back in.