Army Customization, you don't see that in MoM, which is really great.
The world, the quests, the monsters, the graphics + general feeling (FE will have more charisma than MoM)
(I could even add the Zoom option I really like)
The different environments
Boss
The dynasties (wife, child, ...)
Weapons
Maybe mounts (there I don't really know what FE plans for the mounts but WoM was okay I guess with Mounts)
Your sovereign is physically present and can act in fights, move, etc.
Customization of the sovereign won't stop at how many books of one school you posess and a couple perk/flaws
Customization of the city that you can do by yourself (those who played MoM will know what I mean, I think almost everybody here, lol)
The Tech Tree while in MoM Magic is the only research.
Indeed for fun, it really made me laugh, like Louist said it doesn't require DosBox ! LOOOL !!! (hi Louist, long time no see by the way)
+ I would say the economical system which looks like it will be more developped
As well as the diplomatic system !
I think the IA will be more developped too which will be a big + because everybody how dumb the IA is in MoM and how easy it is.
I even want to say the battle system which will be better, based on more attributes than MoM where it stays pretty simple even if MoM has still an advantage with the City Battle System we won't see here.
Now Artefact creation (might still come?), Spells (main goal of the game after all), City Battle (might still come?) and Races (FE's lore is set, we won't see our klackons, Trolls, Elves, ...) and finally flying units or Water Units (We might still get stuff like that) will be the down point of FE compared to MoM.
There, you see ? There's a lot in FE that will be greater than MoM I think but right now with how the spells are, it's a bit dull
I haven't been thinking that much but I'm sure if I think more, I can find more good points for FE =D
Wow, what are you trying to do, sell me the game?
I've already bought it, I don't need to see a point list of all the potential features 
A lot of what you mentioned is subjective and I'm not going to try to change your opinion, but on a few of those I have to really disagree. Of course, FE isn't out, so again, it's all about what we know and what we hope, and what we have seen in Elemental. Ignoring anything graphical related (cause that's not really fair):
Army customization is not that great in Elemental, to be honest. It's a generic person, who is strapped into specific armor and weapons. It doesn't feel like you have a customized army, because everyone feels the same. It feels like a generic soldier, but he has a horse, so he's cavalry, but if he had a spear, he'd be a pikeman (or something). Hopefully, better in FE.
-World, quests, monsters, graphics, FEELING: besides the graphics, which is a no-brainer, I don't believe any of those are better. World, quests, FEELING was boring, IMO. We'll see what FE will bring.
-Different environments? Like swamps, forests, and such? MoM had these.
-Boss? What Boss, you mean the campaign boss? Ugh. But if you mean big baddies, like dragons, then MoM had this beat too (I'd take a Sky Drake over the entire Elemental roster 
-No dynasties in FE
-Weapons - MoM is better, no question
-AI: Now this, hopefully, will be much better than Elemental; that will be a really good benefit, and yes, could be better than what MoM had (weak AI)
The rest, IMO, is either worse or equal to what MoM had. If you think they're better, then that's fine, but I played them both extensively and if Elemental was better, I would be playing it right now. And this is not unwarranted criticism, because a lot of what I'm hearing from the dev's is praising it (Wardell saying that it's a lot more like MoM than Elemental, Shafer or Paxton saying that they and Wardell think it's going to get a really high metacritic score, etc) because of it's new features. If this was the first game, then I'd be a lot more excited than I am right now. But now we'll have to wait and see.
Look, I will be right here praising FE if it turns out to be a great game. I know I have been critical of it, and of Elemental, but that's mainly because I was led to believe it was a different game than what it turned out to be. If I'm wrong about the expansion, I'll say it. But I really want this game to be good, and blindly praising it will not make it so.