gameplay
AC's gameplay has not been duplicated to this day. The noticeable exception being civ 2. The more recent iterations of the civ series have taken a step backwards in some respects. Anyways, since EWOM is not a duplicate of AC it won't do us any good to talk about the specific features of the game, rather one should focus on what the effect those features has on AC.
factions
What did AC do so right about it's factions? The factions were completely static. That is to say, the benefits and drawbacks of each faction was completely immutable. You picked your faction and that was what you were stuck with.
This worked well with AC because it was done so well. Each faction played differently. There were builders, rushers, hybrids, momentum, peace-loving, war-loving, opportunistic etc. Playing Morgan faction and playing Lord's believers was basically like playing two different games. In fact, you don't learn how to play AC as much as you learn how to play a faction in AC. This is good. This fundamental level of difference gives life to the game. Sometimes I don't feel like playing Yang's AC so I play Morgan's AC. This level of difference is what keeps people playing. The most appropriate example for this is DOTA and HON. You have styles, carry, support, push and beneath that you have heroes - a sandwraith plays entirely differently than a swiftblade, despite both of them sharing the same archtype. This sort of layering is what made AC factions so great.
A brief intermission from AC gushing:
The absolutely best system in a game like this has to be fall from heaven a civ4 mod. You have your preset factions but you have leaders that you can change it slightly. I don't think FoH implemented this nearly as well as it should have been but the concept allows for that layering balanced approach of preset factions with a bit of customization on the part of the player.
Unit design
I saw a thread awhile back about how the unit designer should function. Copy AC, seriously.
The amazing thing about unit design is that it allows the player to tailor units to overcome a specific challenge in that game. For example, you are Morgan, happy to make your energy and live peacefully until you discover your neighbor happens to be a bloodlusted eco-feminist named Gaia. You change your gameplay and pick different techs but most importantly, you change your units. You replace all your stock units with ones most resistant to Gaia's strategy.
A system like this allows the player to come up with creative solutions to problems.
Probe teams
This is an absolutely crucial unit that should be carried over. The probe team allows the player to come up with truly creative solutions that most game designers think is impossible. This singular unit allows you to shift how you play the game. Take Morgan for example, you can choose to play a more conservative way with conventional units or you can choose to sacrifice your entire military and play only with probe teams as a sort of bribe everyone free market army.
What is the probe team though? The probe team is a unit with a set of scripted abilities. I'm sure everyone is familiar so I won't list the skill set but you should reflect upon the different roles the probe team can play. Without a doubt, EWOM is a game made for probe teams.
Naming convention
I talked about this briefly in my first post (I think) but what makes the AC naming convention so great is the utility and ease.
You have a default name for your customized unit that follows a formula. The unit's actual properties determine the flavor name. So for example, picking X weapon for your unit might result in the prefix "Shock" while picking Y armor would result in "Probability" as the base and abilities A and B "AAA garrison" the suffix. So in the end your unit name would be something like Shock probability AAA garrison. -I don't think that is a possible combo-
The main point here is that while the player can customize the name if they want. A system is in place that adds life to the game world and has a gameplay purpose.
depth
With balanced factions comes depth. You can employ actual different strategies to win. A big problem is that game developers mistake the choice between right clicking someones city with axemen or swordsmen as some sort of depth. Players tacitly see through this.
The hard part here is balance. Without balance there is no depth. Everyone on multiplayer will tend towards the strategy they can win with. Even if they personally dislike the type of game that makes them play.
So how do you let builders build and rushers rush in the same game? Hard work. Balance is a numbers game that requires testing and refinement.