List of what I don't like about Civilisation II
Lack of granularity of city population (and hence the significance of population loss when cities are captured)
Lack of unit stacking (unrealistic combat - one unit can defeat 50 if they are in the same tile without a city or fortress) (makes the game take longer as there are more units to push around the map)
Lack of granularity in the strength of military units (i.e. one whole unit)
Unit driven exploration
Unit driven espionage
Unit driven sabotage
Unit driven establishment of embassies
Unit driven terrain improvement (very player-time intensive)
Unit driven trade
Unequal diplomacy
Settlers taking a unit of population and food
Lack of a scenario generator
Unreliable "go to" function for units
Unrealistic terrain modification (it's possible in game to irrigated and subsequently transform to grassland the whole Sahara Desert)
AI civilisations building cities in between my well-spaced cities (how rude!)
Inbalanced attack/defence - at the scale that Civilisation deals with (and particularly for the pitched battles of antiquity) there is little difference between attack and defence
Civil disorder - it's just not that fun to manage
Road triple movement rate - not realistic
Railroads give infinite movement - definitely not realistic (I wish my train were that fast!)
Standalone artillery units (a special case of the unit stacking criticism) - does it make sense for a catapult unit to have the strongest attack in open country?
Isometric graphics - why bother?
No technology, intelligence diffusion
Population growth tied to food (rather than medical technology)
No upgrade path for units (other than Leonardo's Workshop)
Weaknesses of the Civilisation series cities model
Being forced to place cities in undesired locations to give them access to special resources or squares with high food production
There is no way to place cities without overlapping (which inhibits growth in the later stages of the game) or leaving unutilised tiles (which is a waste and will sometimes encourage the AI to build on these tiles)
The civilisation model would achieve a perfect utilisation of resources with even placement of cities - this does not reflect how cities grow in reality there are far fewer significant cities in the mid west of the USA that there would be under the civilisation model
City placement is micromanagement, which is dull
Naval production is limited to cities placed by the sea