Combat has changed considerably from civ 2.
1. As already mentioned, winning a battle no longer kills an entire stack.
2. There are now 4 exp. levels of a unit: conscript, regular, veteran and elite. Units gain exp. from fighting, and their starting exp. level depends on whether they are drafted or whether their production city has a barracks.
3. Armies/leaders.
4. Bombardment.
5. Air units have been totally revamped. You don't need to move them around anymore. Tell it to rebase, target a city and boom it has moved there. You can assign it to air superiority missions (unfortunately its broken, I am sure it'll be fixed), or bomb a specific target, or do recon missions.
6. No more annoying petty partisans.
7. City walls have been totally revamped. Only small cities (lower than 6 pop) can have walls, and the benefit is only plus 50%. Larger cities also get larger defensive bonus, but you can easily bombard a city to kill its population before attacking.
8. No more firepower/hp.
9. You can now draft citizens into combat and enter mobilization mode (more shields, but you can only produce military units).
10. Barbarians have been totally revamped as well.
11. No more zones of control.
12. Some units now get one "free shot" at other units when the enemy moves near it.
13. Unique units
14. Generally they have reduced the number of regular units available. Lots of civ 2 units like cruisers, crusaders, dragoons, partisans, fanatics, and a few others are gone.
15. Fast units can now retreat from combat if fighting a slower unit.
16. Units are no longer supported by individual cities
17. The AI have been totally revamped. It is now capable to launching and coordinating an invasion in the scale of 50-100 units (no exaggeration here) attacking at once.
18. Building infrastructure now generally takes longer. That means I can no longer take a whole army of engineers with my army to construct fortresses and railroads instantly in every case (its still possible to instantly build stuff if you throw in enough workers, its just harder).
I am sure I missed a few. But trust me, all the above combined means a very different combat experience.
Now, onto your points:
1. Stacking units into armies. This has already been addressed.
2. Unit orientation. Good idea, but this is not steer panther or close combat. This game is about all the aspects of empire building and combat is only one aspect. There are already enough micromanagement in this game and I don't need more.
3. Air superiority is broken. Air units are now limited to bombardment. They CAN attack naval units and reduce them to 1 strength, but they cannot kill them. I can live with that. Its not realistic, but this is not a simulation, its a game designed to abstract reality to provide enjoyment. What's the problem with building some naval units to finish the job?
4. See #2 and 3.
5. ditto
6. ditto.
Combat is only one aspect of the game. We have a lot more aspects like science, diplomacy, trade, city management, worker management to worry about. If we introduce too many detailed wargame aspects then it will slow down the game a lot. Nice ideas, but wrong game