Civ1 is well-known to have replaced Turks (led by Suleiman) with Germans in the last minute. The first edition of game manual still referred to Turks. As suggested by this Flash of Steel comment ("They probably realised that Germany is the number one strategy game market in the world and Turkey isn’t"), this may be due to the need to appeal to people's nationalistic sentiments.
Civ2 has Inca and Arabs listed in its GAME.TXT. This is also well-known.
Traces of unused leaders can be found among the Civ4 core game's files.
A CivFanatics summary of the files
Non-playable nations in Civ:
In Civ1, the Barbarian leader is Attila the Hun.
Starting with Civ2, the Barbarians may found cities named after historical nomad tribes.
In Civ3, even the Tribal Villages (nicknamed "goody huts") have names that are displayed when the player receives a bonus from them. These are names of history's various more "stable" cultures.
An important new mechanics in Civ5 is the City State system. The world's smaller nations are now represented by these City States.
CivRev has three Barbarian leaders: Gray Wolf (cold region), Brennus (temperate region) and Norte Chico (warm region). Brennus is Civ series' leader of the Celts; Norte Chico is a much more disconcerting case. The character looks like a cross between a dark continent savage and a Carribean cannibal, while the historical Norte Chico is the oldest known civilization in the Americas, named after the region of its discovery (Norte Chico is Spanish for "Small North").
Civ series leader trivia:
Only 3 leaders are featured in all Civ core games: Alexander, Elizabeth and Gandhi. Expand the criterion to include expansion packs and DLC, and there is a fourth one: Geghis Khan.
"Montezuma" is in all Civ core games, but prior to Civ5, the Montezuma in all Civ games refers to Montezuma II, while Civ5 uses Montezuma I. Technically, since Civ2 doesn't unambiguously identify its leaders in Civilopedia or the game manual, Civ2's "Montezuma" can be any Montezuma.
Civ2's male German leader is "Frederick", but judging from his portrait, this is in fact a different Frederick II from all other Civ games. The other games have Frederick II of Prussia; Civ2's is Frederick II, Holy Roman Emperor.
Civ3's Dutch leader is William I of Orange, yet the artwork mistakenly depicts the other William of Orange, William III of Glorious Revolution. This mistake isn't repeated in Civ4.
More trivia regarding Civ2's female leaders can be seen below.
Nations that could potentially be featured in the Age of Empires series:
This part is entirely based upon Sandy Petersen's "Ask Sandy" forum posts.
Before the theme of AoE2:TC was decided, the ideas proposed for AoE2's first expansion pack included the Renaissance.
Sandy's proposal for a second AoE2 expansion pack was themed on Africa. The potential civilizations include Ethiopia, Mali, Songhai, Ghana, Ashanti and Kongo.
His proposal for the AoM expansion pack was to add Celtic Mythology and Aztec Mythology. He calls the eventual direction of AoM:TT (Atlantis worshipping Titans) a "false route", a sentiment many fans must agree with.
AoE3's original lineup included Sweden and Italy. When Ensemble needed to cut 2 nations from AoE3, they decided to remove these two.
The reason to remove Sweden and Italy:
"we had to cut two civs from the game. We wanted to drop civs which had little to do with the New World. Our choices boiled down to Ottomans, Russians, Italians, and Swedes. At this time, the Russians were finally coming into prominence. They rose from being almost nothing re: 1500 to being arguably the strongest state in Europe during the 1700s, starting with their defeat of Sweden in the Great Northern War. The Ottomans were also in their glory during much of our time period - they were clearly the dominant European power during the 1500s, and remained powerful economically and militarily during the 1600s. They did start to decline during the 1700s. On the other hand, the Italians were in a period of eclipse during much our time period - they were bullied by the Ottomans, the French, the Austrians, etc. This really wasn't a great time to be Italian, at least not on a national basis. They didn't really start to recover until the 1850s. One can make a case for the Swedes rising to great power status during the 1600s, but then they fall back down again after the battle of Poltava in 1709, so they didn't get to be a Great Powers very long.
Other games that are related to the Civ-AoE-RoN lineage:
In Empire Earth II: The Art of Supremacy, the African Region is represented by the Maasai and Zulu. The African wonders are Manyatta of the Warriors, Market of Djenne and Sankore Institute. In real life, a manyatta is simply a hut the Maasai people's young men live in, and Djenne and Sankore belong to Mali. "Market of Djenne" is depicted as the Great Mosque of Djenne plus a few stalls, not unlike how the Kremlin is always represented in strategy games by Saint Basil's Cathedral.
The Japanese console versions of Civ1, developed by Asmik, replaced the Zulus with the Japanese. These are the Super Famicom / SNES version, and the Saturn and Playstation versions. The SNES version is the only one that's been published outside of Japan.
Call to Power nations that are not in the canon Civ series:
Antiquity: Assyrians, Hebrews, Phoenecians
Pacific: Indonesians, Polynesians, Hawaiians
British: Scottish, Welsh, Irish
Colonial: Australians, Canadians, Jamaicans, Cubans, Brazilians, Mexicans, Nicaraguans
Considering how important civilizations like Arabs and Babylonians are still absent, the Call to Power series' civilization lineup began to seem like a Borgesian taxonomy joke. This joke will be further exposed in the following part.
The curious case of Civilization II female leader names:
Civ2 is the only Civ game to allow the player to choose between one male leader and one female leader for each civilization. However, given women's social status in patriarchal societies, iconic female political leaders can be difficult to find for some nations. Nonetheless, the fact remains that some female leaders in Civ2 can be argued to be very poor choices, or at least, have never been political leaders:
French: Joan of Arc (fans have complained about her leading the French in Civ3)
Americans: E. Roosevelt (First Lady)
Babylonians: Ishtari (goddess)
Japanese: Amaterasu (goddess)
Greeks: Hippolyta (mythological figure)
Persians: Scheherezade (legendary figure)
Viking: Gunnhild (historicity disputed)
Sioux: Sacajawea (Shoshone companion of the Lewis and Clark Expedition)
Aztec: Nazca (name of Nazca culture)
Zulu: Shakala (completely fictional?)
Weirdness first show up in the Playstation version of Civ2, where the names of 3 female leaders are changed:
Viking: Gyda (first queen of united Norway)
Zulu: Nandi (mother of Shaka)
The former 2 are reasonable changes. The new Aztec female leader is strange: the game claims Nezcaltiloyan to be "the Aztec Mother Earth goddess", which is entirely wrong. A Google search yields few results for the word, one of which is from a 1877 book titled "On the Art of War and Mode of Warfare of the Ancient Mexicans". It says Nezacaltiloyan means "the place where I grow", and refers to places of youth education for the Aztec.
As the final proof of the Playstation port's sloppiness, in the actual gameplay, Gyda is spelt Gyde, and the female Aztec leader is again called Nazca.
Then we have the CtP series. Not all leader names remain the same between CtP1 and CtP2 (for example, CtP2 changed the Chinese leader from Mao to Sun Tzu), yet the CtP series inherited some of Civ2's more questionable names like Sacajawea, Scheherezade, and Shakala. CtP continues to ignore the many politically influential female figures in Japanese history, as the Japanese are now led by Murasaki Shikibu, the author of Genji Monogatari. Best of all, the CtP series don't have the Aztec; instead, Montezuma and Nazca are the proud leaders of the Nicaraguans!