Civilizations: In reality it's more Continental Regions. They're basically templates a player chooses from. Each have their own tech tree, building and unit sets. This is different from Empire Earth 1 where you had one building set and one tech tree. In EE1, strength came from the Civilization bonus editor and unit stat boosting throughout the game. I can see why people are put off on this, because EE1 had a large list of bonuses to choose from which gave players different ways to approach the game and every unit could be boosted in attack, speed, health, range, area damage, etc.. Which can be done as the game progresses. There is a civilization editor in EE3 though and you can select through a point system what researches you start with and what units you start with. So you can inject some variety into your skirmish games.
Epochs: Around 5 of them a departure from EE1's 14 epochs. Ancient is EE1's Bronze/Dark, Medieval is EE1's Middle Ages, Colonial covers EE1's Renaissance through Industrial, Modern covering Modern, and Future covering Digital/Nano.
Path Finding: Pain in the ass. Made more obvious in the game with how sluggish units are and can be frustrating at times trying to get anything to move through terrain.
Resources: Down to Wealth, Materials, and Research. Less time spent of eco management to encourage more focus on combat I guess.
Combat: Follows the same Rock, Paper, Scissors formula like EE1. So no change there. Naval and Air combat is still there, Mechs still exist too.
Dialog: Tad annoying and childish, lot of dad jokes.
Graphics: Nothing really pops out and wows you. Characters look like dwarfs. It does have weather, seasons, and the environment looks nice. Civ color though seems to drown out a lot of detail on units and buildings.
Music: Didn't really pay attention, but music does change when you enter combat.
I think had they not called this game EE3 it would have been saved from being compared to EE1. Maybe even standing on it's own.