The most fundamental difference between Civilization II and Freeciv is that Freeciv was designed from the start as a multiplayer, network-based game, which has many implications with regard to the game mechanisms. For instance, while the United Nations Wonder could force AI races to have a certain foreign policy, it could not conceivably constrain real human players, with a result in a reworking of what the United Nations might do. Thus the United Nations Wonder has an entirely new result, the Marco Polo's Embassy Wonder and Eiffel Tower Wonder are removed. The Great Wall Wonder does not force other nations to offer cease-fire or peace, nor does it aid against Barbarians (which do not exist in Freeciv). There is no concept of peace between nations.
Many other features of Freeciv differ from Civilization II because Freeciv was originally developed to match Civilization, and some Civilization II features are not (yet) implemented.
To simplify implementation, the number of terrain specials was reduced. Where Civilization II has 21 specials possible for 11 terrain types, Freeciv has now 12 terrain types with exactly one special possible for each. A terrain square either has, or lacks, the special for that terrain type. Some of the specials were renamed and other adjusted for balance. A fundamental change is that rivers are no longer special features of land squares, but terrain types of their own. Unlike Civilization II, in Freeciv, once a player has seen a terrain square, that nation will always see what is in the square.
The government type Fundamentalism is not implemented, nor are Fanatics. Several balance changes have been made to other government types: A Despotism has no limit on the number of military units per city devoted to martial law, and a Communist government now has modest but invariant corruption. Settlers and Engineers have changes in the support they get from cities. Corruption in Freeciv loses only trade points, but not production points.
A different approach to nuclear energy is implemented. Nuclear Plants now have no chance of meltdown from civil unrest, making them effectively as useful as Civilization II's Solar Plant. Thus the Solar Plant is removed, and its enabling advance Environmentalism as well.
After starvation, a Granary will restock itself to half full. A Supermarket in Freeciv increases the food production of all irrigated squares; the Civilization II concept of double-irrigation does not exist. The units Elephants, Crusaders, and Paratroops are not in Freeciv. There are no Barbarians in Freeciv, and Villages will not produce them. Fighters will not defend cities from attacking air units. Units other than Marines may not move directly from sea units into undefended cities. Airbases no longer exist. The Nuclear unit requires only Rocketry, without Nuclear Fission as well. Partisans are only created for the original owner of a city. The chance of a Trireme being lost at sea is always 50%, not modified by other advances. Diplomats and Spies do not (yet) get advantages from veteran status.
Several new things have been added: The commands Auto-Explore, Auto-Settler, and Auto-Attack.