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The major thing hexes have going over squares has to be the more sensible path cost it provides. A hex can have a cost of 1 for each direction, while a square-based system ought to have something closer to 2 per major direction, and 3 per diagonal to be 'fair'. (I use 2 and 3 because they are are a good approximation of the difference between 1 and sqrt(2), and integer math tends to be faster than floating point.)
For what it's worth, Toady does (at least in some cases) consider the sqrt(2) case for diagonals. And yeah, that problem would exist with hexagonal prisms anyway, since you have cells bordering on edges and points as well as faces... or at least on edges, anyway.
Hexagonal prisms would make multitile creatures a bit weirder in that the axes simply aren't treated the same. Imagine a multitile creature (tall and wide and long) in a hexagonal prism system getting knocked over; there's no particularly good way to represent it. With cubes, you can rotate along the axes just fine and nothing at all has to change.
Quite frankly, I think squares/cubes simply look better for this sort of game, because it involves lots of manmade construction. In games like these, squares are usually better, since buildings and roads and the like tend to be very, very rectangular. Note that most hex tile games either take places largely in natural settings where this doesn't matter (like war games), or in places where the manmade stuff is so large in scale that you can fudge the edges without any particularly odd consequences (rarer, but an example is Fallout).
Just a major factor, a square touches 9 things, a hexagon only reaches 6.
The problem here is that you have to define "touching". A square is adjacent to four other squares, and touches four others at vertices. A hexagon is adjacent to six other hexagons, all equally. So for a few reasons, hexagons wind up being easier to work with sometimes.
Of course, we're not dealing strictly with hexagons and squares here, hence my thinking that hexagonal anything isn't a great idea.
It exists "per layer", but at the cost of making the world's representation more irregular and asymmetrical in general.
Whether or not the OP was suggesting this for aesthetic reasons is moot, as there's no way the game's representation of the world itself is/will/should change just because one lets a small minority of players build fortresses with layouts they like slightly more. What's paramount is how well it actually works.
I said you can't stack copies of a hexagonal grid in a manner which creates any sort of regular structure. This is entirely true. It's uniform, but it's not regular, and not even particularly close to it.
Dude, you have some serious i'm-right-you-go-fuck-yourself-issues you need to work with. This is a suggestion thread in which the OP made a suggestion(!), you stated your opinion on the matter and others do not agree. This is all good, there is no reason to convince anyone of your opinions superiority.
I'm trying to clear up mathematical fact here. I spent enough time looking stuff up about this that my head sort of hurt. I don't expect anybody else to have done that sort of thing, so I'm trying to make sure I'm getting facts across right.
The reason I made a big deal about the "regular structure" bit is because you were implying that stacking hexagons "works". I was trying to state in what ways it doesn't "work" compared to, say, cubes.