I've changed Civ leaders on this map by opening the Worldbuilder Save file with notepad or wordpad, deleting the old Civ name LeaderType=LEADER_LOUIS_XIV, and then putting in the new name from the New Leaders mod (or just the vanilla alternate leader - LeaderType=LEADER_NAPOLEAN, for example), and then changing the next line after that - LeaderName=Napolean. (The first determines the pictured leader I think, the second is the name that you see, so it can be whatever you want) - That's also how you can change the victory conditions and other stuff (like others have said). So I imagine that would be the same method of putting in new Civs, just substituting the old ones with the new. Edit CivType=CIVILIZATION_WHATEVER_NEW_CIV and all the rest of the lines that pertain to the new civ - team color, adjective, etc. It looks like this:
BeginPlayer
Team=9
LeaderType=LEADER_NAPOLEON
LeaderName=Napoleon
CivDesc=French Empire
CivShortDesc=France
CivAdjective=French
FlagDecal=Art/Interface/TeamColor/France.dds
WhiteFlag=1
CivType=CIVILIZATION_FRANCE
Color=PLAYERCOLOR_DARK_BLUE
ArtStyle=ARTSTYLE_EUROPEAN
PlayableCiv=1
MinorNationStatus=0
StartingGold=0
StartingX=58, StartingY=51
StateReligion=
StartingEra=ERA_ANCIENT
CivicOption=CIVICOPTION_GOVERNMENT, Civic=CIVIC_DESPOTISM
CivicOption=CIVICOPTION_LEGAL, Civic=CIVIC_BARBARISM
CivicOption=CIVICOPTION_LABOR, Civic=CIVIC_TRIBALISM
CivicOption=CIVICOPTION_ECONOMY, Civic=CIVIC_DECENTRALIZATION
CivicOption=CIVICOPTION_RELIGION, Civic=CIVIC_PAGANISM
Handicap=HANDICAP_NOBLE
EndPlayer
That's how I changed the French leader from Louis to Napolean - so as you can see, there are lines there that determine the Civ itself, and a lot of other factors - the name of its flag file, the era it starts in, whether or not it's playable, its state religion (notice above that it's blank because France hasn't adopted a religion yet), etc. So make your changes, save the text file, then start up the map and pick the first listed civ (so you have first turn, that way none of the AI civs found a city). When you get in to the game go to Worldbuilder, move the civs to wherever you want them to be, then save the map and call it whatever you want.
I'll try it out myself some time in the future and see if it works, but if anyone else has any success with this lemme know.