City Radius: A city may make use of all tiles within its radius, not just a certain maximum number. With this caveat, only those tiles actually under a city's control. Which tiles are under a city's control depending on the city's culture. So if a city has a five tile radius, then that city would be able to exploit tiles 5 deep.
Which does kind of throw a monkey wrench into figuring out city placement, no ?
Conquest: A player may choose to occupy a captured city instead of annexing it. If occupied it is to be returned to its original owner upon agreeing to a peace treaty.
This is different from being able to trade cities in diplomacy Civ-3-without-expansions style how ?
Technology: Once a discovery has been made, a technology invented, it tends to spread. Thus, for every civilization that knows a technology other civilizations can gain a bonus when researching that tech. Thus if the bonus is set at 5% of available science production, three civilizations knowing the secret of a particular tech would mean any other civilization researching that technology would gain a 15% bonus to the science production dedicated to the task of researching it. In short, the more people know of and about a bit of knowledge the easier it becomes for others to learn about it.
This was implemented in Civ 2.
Retreats: An unit, fast or slow, being defeated in battle may choose to retreat. The chance of successful retreat depending on unit speed, comparative technology, and how damaged the victorious unit is.
This is implemented in Civ 3 for fast units with enough movement left, which to some extent depends on damage IIRC.
Combined Arms: Two or more units may combine their strengths, with different types of units having a synergistic effect. So that musket and pike together, for instance, would have an advantage over enemy units they would not have alone.
This is implemented by having separately varying attack/defence values pre-Civ 4.
Mines: Mines may not be built on grassland, flood plains, or prairie.
Irrigation: Renamed farms. Restricted to grassland and flood plains.
How does this benefit the game ? It reduces flexibility, that I can see.