I see your experiment with movement. I thought about it too, but rejected - since it'll be brilliant result, but the mechanics inside will be overcomplicated, IMO - so was a decision to try without it, yet (probably).
The movement part of the mod is one of the areas that has worked very well. The foot units I mentioned before are the slowest land units, horse units and early wheeled units mostly move 4-6. Later mechanized units can move up to around 12. These are all road moves, with roads being set to subtract 1 move per tile in the editor. Each terrain type has their own move factor. For example, plains use up 3 move, deserts 4 move, hills 5 move, jungle, something around 8 move. For some unit types, I gave them the move as roads ability for some of the terrain types, such as the light infantry above in plains, grass & flood plain terrain. The real surprise was that the AI was able to use these changes. In fact, the AI kicks butt

It's one area where I was able to improve AI performance and make them more of a challenge.
Not sure. City population is limited, and charm has effect 1 turn only.
I was under the impression using CHARM would make a unit that could attack buildings only, provided the buildings had "CHARM barrier" checked, and that CHARM equipped units would be able to attack buildings as long as there was at least one left with that barrier setting checked. I figure, make all regular buildings (not wonders) "CHARM barriers" and these CHARM equipped siege engines would then be able to attack the city's buildings till they are all destroyed. I had though of just making city walls "CHARM barriers", but walls are only useful for towns. In my games I hardly ever build walls because they go obsolete so quickly. I notice that few AI towns I attack ever have walls, also. So a unit designed to be a wall breaker would be a waste.
Not sure about the lethal see bombardment. Any catapult/ballista won't fire a rock/arrow of appropriate weight over so long distance - seems like. And, OK if ship is close to the shore - it means it'll unload troops - and artillery should be in the safe place (safe as possible, of course). Probably I'm mistaken somewhere?
The main limitation would be being able to hit a moving ship with a catapult. That would be tough. But the missiles thrown would be more than enough to sink a vessel. Especially one of the oared ships which were very lightly built. They had to be that way to keep the weight down so oars could move them about adequately. The Greek trireme had hull and deck planking of between 1 and 2 inches thick pine. You can kick a hole in this with your boot

A typical catapult projectile was 8-20 lbs, which would easily punch right through the side or the deck and bottom of a galley and sink it. The cargo ships, being sailing ships and having to carry heavy loads, were more stoutly built, and would be harder to sink. In Classical and Roman times, there were catapults capable of throwing 150 lb rocks and ballistas capable throwing missiles 20 feet long and a foot thick. No ship in existence then could stand up to such projectiles. Alexander mounted siege towers and catapults on ships (barges essentially) for attacking a coastal city. His descendants mounted these weapons on ships also. A couple of the ships being famous, and huge, larger than an 18th century fist rate.
Eventually, I would like to incorporate all of these in the mod I'm playing around with. Giving these ancient bombard weapons a sea unit killing ability is also useful in making shore bombardment more risky and adds to the game play some that way. I've found the AI have no problems using ship mounted bombard weapons to attack land and sea units, cities and even terrain improvements. If I can get them to use land bombard units against bombarding ship units, that would be great, and using lethal sea bombardment appears to encourage this from what others have found of AI use of artillery. There could also be an area for CHARM ship units, to mimic Alexander's siege barges, for example. All this needs to be tested. This is part of the reason I was interested in find the material recently discovered about getting the AI to use bombarding, in addition to making land artillery units the AI could use.