- Watch Towers equivalent to Age of Empires II's Outposts (only for observation, no attack, and no upgrades) were created before being scrapped. Confusingly, the equivalent of the previous game's Watch Tower is called Outpost here.
- A Fortified Wall upgrade was created (and appears extensively in the Campaigns). However, it came with different interior and exterior sides... and the computer could never figure which was it when building or upgrading an existing wall, so it was scrapped.
- Italy and Sweden were to be playable factions until fairly late in development. This is why the game has the Elmeti and Swedish fusilier as mercenary units, and possibly why the Horse Artillery is a common unit in the Industrial Age (in reality it was an innovation of King Gustav II of Sweden, although other countries copied it later). The latter was eventually added in the Definitive Edition.
- According to developer Greg Street, Italy would have a unique design where the player could elect between subclasses standing for different historical Italian republics (Genoa, Milan, Venice), with their own unique units and bonuses. While Sweden was "a celebration of Gustavus Adolphus and all of his military innovations, with beautiful houses."
- According to lead designer Sandy Petersen, there were plans to include Native American playable civilizations already in the vanilla version but they were prevented from doing so.
- Petersen wanted to include the Incas as the fourth playable faction in The Warchiefs, but they were scrapped by other leads due to time and art constrains. One of the four had to go, and they thought the Incas the least interesting and harder to find information about. They were finally added in the Definitive edition, a decade and a half later.
- Petersen later outlined a second expansion set in Africa, with Ghana, Songhai, Ethiopia, and Kongo as new civilizations. However, the idea of setting the second expansion in Asia prevailed and the African expansion was retooled into the African Kingdoms expansion of Age of Empires II.
- Still wondering why the Ottomans are included in a game about the colonization of the New World (and the East Indies in the expansion)? It's because there were going to be maps based on Europe and the Mediterranean, but they were cut for time and due to having trouble incorporating the "build a colony and ally with the natives" High Concept to the Old World.
- A pre-release map list included an Andes map and described it as an Inca city in the center that you have to control to win, with neutral "warlike" Huari strongholds scattered in the country around it. In the vanilla, the Andes are not included, the Incas appear as native villages in Pampas and Amazonia only, and the Huari are not included at all (although there is a building in the Pacasmayo campaign scenario and the Editor that is probably the planned stronghold). The War Chiefs introduced an Andes map, but it was a standard map with mountains on one side, a trade route on the other, and Inca villages scattered throughout.
- New, map-specific resources were planned including Cotton, Tobacco, Sugarcane, and Spice.
- The first outline of the game began firmly in the Renaissance era, with several units available in the Discovery Age (swordsmen, archers, pikemen, knights, ships, and even a small cannon) and skins matching with every new age. Nearly all this early gameplay was scrapped, players were banned from making military units in Discovery (other than Militia and pets), and some unit lines were pushed into the Colonial age and beyond resulting in Anachronism Stew.
- The scrapped Italians were going to excel in this early warfare and become weak in later ages. They'd have their unique, stronger versions of the Knight (Elmeti) and Crossbowman (Genoese Crossbowman, complete with a large pavise); a generic cannon combining the roles of Falconet and Mortar (which became the Lil' Bombard in The Warchiefs), and a Mounted Crossbowman that behaved like a mix of Horse Archer and Dragoon.
- The Italians would also have a second Settler unit specialized in building structures, called the Architect.
- Of the Swordsmen, only the Spanish Rodelero and the German Doppelsoldner survived into the final game. The Italians, Ottomans, and Russians were also going to receive their own versions.
- The Musketeer first became available in the Colonial Age (as in the final game) but had period-accurate Tudor clothing, independent powder bags, and a morion helmet. This skin still exists but it's been replaced in-game with the one originally made for the following Fortress Age version, who wears a Cavalier-era uniform and hat; this had a cascade of effects resulting in the original Industrial Age skin, with breeches and powdered wig, appearing in the Fortress Age, and the Imperial Age skin (in Napoleonic top hat) appearing in the Industrial Age and having no visual difference with its Imperial upgrade. Several other units including Janissaries, Dragoons, Horse Archers, and Cuirassiers, also have additional, more period-accurate skins that don't show up while playing.
- It is possible that this skin wasn't intended for the Musketeer after all, but for a separate archaic gunpowder unit, called the Arquebusier.
- Dutch and Germans could train Musketeers, as revealed by their voice files.
- Dutch could train Crossbowmen.
- Russians could not train Musketeers.
- Portuguese could train Falconets.
- A Medieval-looking bowman was created in addition to the Crossbowman and Longbowman, presumably as another civilization-specific archaic infantry.
- Spahis were the main Ottoman cavalry instead of Hussars.
- Heavy Cannons were created in the Arsenal, while the Factory produced Gatling Guns.
- Dragoons (or possibly just upgraded Dragoons) were armed with a blunderbuss instead of pistols.
- The Ruyter was called the Reiter and shared by Dutch and Germans.
- A Zweihander unit (probably a Discovery version of the Doppelsoldner) was created, then cut. The visuals were recycled into the campaign-only Boneguard Swordsman.
- A steamship was planned for the Imperial Age, presumably similar to the Ironclad introduced in The Warchiefs.
- A "Colony Ship" of unknown function was planned.
- A ranged infantry Mongolian mercenary was planned.
- Some cheat units without cheat codes in the editor are "fossil units" that were designed but were not implemented in the game.
- A non-playable hero "Neamaltha" (name shared with a 1817 Seminole chief) was made, but cut from the campaign.
- The Trireme and Fortress from Age of Mythology were going to appear as easter eggs.
- Planned wild animals cut include javelinas (which appeared in the previous game, but were replaced with tapirs), crab seals (partly coded and with no sprite attached, were going to appear in Patagonia), and ducks appearing either on land or water (only non-interactive flocks flying above are finished).
- Additional or alternative native units like the Nootka Knife Fighter and the Comanche Lancer, whose icons are still in the game.
- The Asian Dynasties has an unused "native mercenary" version of the Conquistador (the kind that is sent with a card from the Home City) in addition to the "native" kind that is trained at a Jesuit trading post.
- According to producer Bruce Shelley, the game was going to be launched under a different name, but Microsoft prevented them from doing so.
- The last page◊ of the hardcover artbook that came with the collector's edition of the game shows Roman numerals extending from I to V, with I through III underneath images from the boxart of the respectively-numbered games in the series. The IV is underneath a picture of a Vietnam-era American soldier, and the V is underneath some variety of Space Marine. Whether IV and V were concept boxart for future games or just wishful thinking remains to be seen. Ironically, it ended up being somewhat prophetic, since Relic Entertainment (developers of the Space Marine heavy Dawn of War) wound up developing the fourth game.
- The Italians's de-facto Home City was Florence (hence the Florence cathedral model used in Lisbon and Seville).
- Several Home City technologies were planned as normal technologies before being replaced with Home City cards or removed.
- Playing against the same civilization in skirmish mode was originally possible.