Other areas that have changed significantly are e.g. trade, diplomacy and espionage.

Diplomacy in the newer games has a lot more freedom and variety in terms of the deals you can make, what you can trade for what with the AI, etc., but you can't directly exchange technologies any more. (At least not in Civ V.)

In Civ I and II, caravans and diplomats/spies used to be units you moved around the map manually. Then there's the whole city states thing since Civ V (I think), strategic resources that are required for particular units or buildings, significant changes in how happiness/approval is managed, as well as several victory types apart from conquest and space race.

In 90's Civ games (except for SMAC) all the civilizations were also essentially identical in terms of gameplay, except for AI leader parameters and diplomatic stances. Newer games in the series have more differences between civilizations in terms of strategy, at least in theory.

Basically, the core idea is still the same but the details and many individual mechanics have changed a lot.

And then they decided that Workers should be replaced with Builders, turning Civ into a micro-management game :(

While considered 'experimental' this is state of the art in FreeCiv:

https://freeciv.fandom.com/wiki/Multiplayer_II_Dragoon_Summa...

And this giving an overview of the development up to that point:

https://freeciv.fandom.com/wiki/Multiplayer_II_Navigation_Pa...

It's not stuck in 1990. Actually rather fun to play against humans, AI still meh.

Civ 2's limited sight distances and "every unit in a stack dies if one unit loses a fight" are pretty good anti-stacking measures until you're well past the inevitable victory watershed line of a game.