Well the ability to have a Custom Trait, UU, UB, Starting Tech Combo would be good (perhaps that game gets no entry in the HoF File (or is entered as Cheater, Altered, etc.)) and is enabled for everyone or no one in multiplayer (it is one of the game settings.. allow Custom Combos)
You could even have Totally Randomized combos for the AIs (so you may end up sharing a continent with a Philosophical Industrial Montezuma starting with Agriculture and Mining a Keshik UU and Stock Exchanges v. a Charismatic Aggressive Washington with Mining, Mysticism, Praetorians UU and Sacrificial Altars)
OK definitely a good idea... Just make it somnething that has to be allowed at game setup (for Multiplayer) and goes in the same Hall of Fame as things that have been World Builderized
What you also need is 'skins' so that for a standard (non-Altered) game you can change not just the leader+Civ Name but also the Leader Picture (pick from a list), banner (likewise), Default City name (a list of lists), UU name (write in), and UB name (write in).
So if you want to play a Hebrew civ, and you figure that Aggressive + Spiritual, and a Swords UU fits them well.... then pick thae Aztecs, and change
Civ Name=Aztecs->Hebrews*
City List=Aztec->Hebrew/Israeli city list**
Banner=Aztec-> (bunch of others)**
Leader Name=Montezuma->David*
Leader Picture=Montezuma->Saladin?Ramses?Cyrus?Just the Banner?**
UU name=Jaguar-> your choice*
UB name=Sacrificial Altar->your choice*
* you type it in
** would be from a list of things available
And wala a Civ of your Choice
(Note could also be done with Existing Civs... you want to play Germany but think they are better represented as Industrial+Aggressive, Pick Napoleon, change the City list, Civ name, Leader Picture, etc.... you will lose the German Assembly Factories and the Panzer, but you will gain the 'Prussian gunmen' or whatever you choose to rename the Musketeer)
Or you could want to play a Civ but with no particular set of traits in mind... have the Computer pick a Random Civ+Leader, and then you change the names, Leader pictures, etc. to fit those of the Civ you want...
Or play both 'unbalanced' and 'skinned'.. That way you are always playing as 'the Scots' but they could be Financial Protective with Assembly Plants and Praetorians starting with Mysticism and Fishing, or any other combination that the computer randomly selects for you.
With those two methods of cutomizing: 'recombining' and 'skinning' the game would be Much more interesting and it should be in the Game setup [talking to those who talk of XML]