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The problem here is that of saving knowledge. If you save all the men in the division you already have trained tank crews and trained support crews. That makes it much quicker to put a division back together then if they all have to train to work together, as long as there are replacement tanks/vehicles.

But as long as reinforcements is as dirt cheap as it is in HoI3, even 1% strength wouldn't be enough to represent the actual industrial cost of all lost vehicles and heavy equipment.

Precisely, there's no way to represent the actual conditions that would be created, neither technically accurately ( due to a lack of distinction between men and equipment) or abstractly through deductions to divisional strength (due to reinforcement cost being too low for IC-intensive units).
 
1) Any brigade landing in a non-port province will automatically lose 50% of its max org.

2) Any brigade landing in a non-port province will get the "attack delay" modifier. The same one brigades get after attacking.
That would be a good start. For simplicity, the AI could be exempt from these penalties, although it could be switch-able in the options. There is no reason to make things harder for the AI, but there are MANY reasons to make things harder for the player.

As far as evacuations are concerned, IMO they should always involve a STR loss as long as there are enemies in nearby provinces. Embarkation should also take more time, i.e. it shouldn't be instantaneous.