First off by people "making" their own civ its more of a customization, just think of AOK/TC and have the ability to choose a couple unique techs, rename techs (tech costs & function stay the same), choose a graphic pack for their units and buildings (Greek pack looks different then Egyptian), and maybe a unique unit.
The gameplay should be balanced as the unit effectiveness and basic technology stays the same. The only things that would make this unbalanced are:
Technology: (thats why you can only choose a couple for different areas)
Unique Units: (uh yeah they're unique, most likely stronger then regular units but its not like you can build them quicker and cheaper then regular ones)
In a way ES did this in AOM its just we choose what we want to be stronger in. And no you cant "supe" up your whole civ by adding 999+ for its attack, armor & LoS. In fact you cant even mess with that stuff unless in scen ed for that scenario. However I do agree that though I like this idea it just wouldnt work in an AOE series game.
Also another thing id like to add. AOE, AOK & AOM generally takes place in Europe. Nothing bad about it (in fact a LOT of history has taken place in that area, and besides it's much more fun). Again, Thank You for reading this.