1) I liked the way Civ3 and 5 treated seige too. Especially Artillery and later seige.
The earlier seige, one could expect mounted units to race up and attack, but Artillery can fire from miles away and shouldn't be reachable in the same turn.
I too started to find Artillery becomming useless after aircraft emerged. Especially, when going from island to island. Carriers are far simpler to manage.
2) I don't know if this is possible to mod in, but in Empire Earth, we could build free standing Anti-Aircraft guns to shoot down fighters and bombers. Is there anyway to create an improvement that includes an AA gun?
It would not be a unit, and a worker could build it on any non-mountain land tile. Maybe, something like a 25% chance to damage the aircraft? Perhaps, subtract 1 prod from the tile?
Even an improved one costing 2 prod/tile, but a 50% chance to damage, to encourage these to be built in hills.
In EE, we could build dozens of AA to protect a specific border.
3) I like the idea about subs used as pirates. Unless another sub or dest is nearby using active sonar, it isn't easy to identify whose sub it was in real life.
I hope the submarine images will be corrected too.
The Submarine in the Civilipedia should be an early WW2 sub, like the famous German U-Boat. The image shows this, but the stats don't. The U-Boat couldn't carry 3 nuclear missles. Those would be Boomers or Ballistic Missle Submarines which would carry 16, 20 or 24 missles, but nevermind that now. The third type of Submarine would be the Attack Submarine, which would be the modern equivalent of the U-Boat. The Civilopedia has the name correct, but uses the image of a Boomer.
The civilopedia seems to cramm these 3 units types into 2 units.
Since, you did a Hunt for Red October mod, you are familiar with the 688 fast attack submarine (USS Dallas) from the movie. That is the modern upgrade from the U-Boat.
Also, they would require different resourses. To summerize:
U-Boats requires Oil and upgrades to Fast Attack Sub. Correct image. Use the image from "Submarine" from the Civilopedia.
SSBNs require Uranium and can carry 3 missles. Correct image. Use image from "Attack Submarine" from the Civilopedia.
Fast Attack Subs require Uranium. Use image a real fast attack image to add to the Civilopedia.
If someone doesn't want to overcomplicate the sub field by adding even more, that's fine, but those 3 types should be the minimum. It seems silly to use U-boats to launch nuclear missles at modern tanks on the ground.