I take issue with the idea that you can 'stop' a plane in mid-flight.
Idle circling around the area. They spot the Submarine, then fly around it since the sub can't shoot back as they relay its position to you.
Also weird is how things can't drive under planes.
They don't want to get bombed.
Andy's CO power
Andy's CO power repairs units. In Advance Wars most units are actually groups of 5 (for example, if you build a "light tank" it is a group of 5 tanks), and damage is represented by some of the members dying.
My god, the soldiers are all robots! This explains everything!
On a similar note (also possibly Fridge Horror)... Repairs to tanks, copters, and such could be hand waved as the drivers are fine, it's just the vehicles that need repair. However, how do you explain Infantry/Mech? Especially when you have them repairing on a city instead of with a CO Power? Are they "refilling" their unit by taking civilians out of the cities?
Sensei's power is a paratrooper airdrop; something similar could be in place to reinforce city-occupying units.
In Days Of Ruin, the factories are fully automated and build what are implied to be unmanned drones...that's all fine and dandy, but then tell me, why are human solders shown driving them? Furthermore, how do the factories build INFANTRY units?!
The factories have your soldiers in them once you capture and secure it. Factories fund and supply weaponry to the soldiers.
Speaking of Days Of Ruin, I find the concept of CO units a bit weird. No matter how may times the CO unit dies, the CO themself is always completely unharmed and back at the HQ within the space of a single day. I can imagine Will jumping out of a ruined tank or bailing out of an exploding plane, but how on earth does he escape from a sinking submarine? Furthermore, when the CO "boards" Infantry or Mech units one would assume they are grabbing a rifle and tagging along to fight in their squad, meaning that when the infantry dies, the CO unit is being repeatedly shot until they can no longer remain conscious, and yet they are still good to go the following day. Furthermore, how does ever single CO in the game (even as young Isabella and Penny) automatically know how to pilot tanks, ships, planes, and fire rifles & bazookas.
In fact, the entire series has been a bit weird with COs, in the first 3 games everyone spoke to each other as if they were talking in person and occupying the same space despite being implied to be on opposite sides of the map inside their H Qs. For example after AW 2's "Lash Out" mission Nell tells Sami to "Drag that brat over here" only to find that it was a dummy, did she drag it through the ocean or something?
Naval units and fuel
Why do naval units use fuel even when they're not moving and sink when they run out? Who would design a ship that lacks the buoyancy to stay afloat without fuel? For that matter, why do air units use fuel even when they're over land and not moving? Wouldn't it make more sense to be able to land an aircraft when it's not in use, since it doesn't waste fuel and makes said aircraft harder to spot? (I understand that the former is for gameplay purposes, since a naval unit stranded where land units can't attack it would make maps without any ports or airports unwinnable, but being able to land an aircraft would actually be pretty cool and add a new layer of strategy: "Should I land this helicopter for now and risk making it more vulnerable, or should I use precious fuel to keep it in the air?")
Out-of-universe, boats self-destruct when they run out of fuel to avoid map clutter - if they're out at sea, an APC can't reach them. In-universe, they're probably being scuttled to protect military secrets (com-codes, maps with positions of friendly units, stuff like that). Also, since you mention buoyancy, ships often require bilge pumps to stay afloat during long trips... but we're talking months/years, not days, so that probably doesn't factor in.
In Black Hole Rising, Mission 29 ("Rain of Fire") has a gimmick where a volcano would erupt daily, causing damage to any units sitting in an unlucky spot. Whose idea was it to build that many cities at the base of an active volcano?
If your question is about the number of cities, maybe it is to represent the idea of many people living here (as well as providing some strategic objectives); if it's about the idea of building a city at the base of an active volcano, well, that's Truth in Television: there are about 4 million people currently living at the base of Mount Vesuvius, fully aware of what happened millenia ago.