I did not purchase ETW or NTW and so cannot speak to those, and I played M2 for a week before giving it away.
But in RTW, the 3D map did two very bad things for game-play.
First, it insured that most battles would simply be skirmishes that eventually had to lead to a siege, as province resources are held by the local city. On a 2D map, every battle was a fight for the province, and many a campaign came to an early, disastrous end simply because you lost key provinces early (as anyone who played the 1580 Oda campaign in STW can attest to).
Second, it presented more options to the AI than it could possibly handle, and led to much aimless wandering by AI stacks with no clear purpose, and a lot of wasted time on the AI's part, particularly with pathfinding issues. In STW, for instance, it's a guarantee that if you leave a weak province near the front, the AI will find it and attack with overwhelming force.
ZOC issues were never handled correctly, IMO, especially for naval battles. Any incursion, either by sea or land, into a neighbors territory without access rights, should, by all standards, lead to a declaration of war.
I much prefer the 3D map in terms of looks, but the 2D map in terms of gameplay.
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