In other words, if two creatures are adjacent on nodes sharing a square face, they're farther apart than if they shared a hexagonal face. How do you handle a situation like this in a game? It's not very clear at all.
If I'm reading that Wolfram Alpha article correctly, the distance between two units on cells sharing a hexagonal face is √6 whereas the distance between two units on cells sharing a square face is 2√2, assuming that each unit exists in the center of the cell, which is reasonable. In terms of a ratio, the ones sharing a hexagon are about 0.886 times as far apart from each other as ones sharing a square. This difference in distance is significant - almost as significant as the difference between the distance between two adjacent squares and the distance between squares diagonally.
Wait, so what's the practical difference between defining adjacent tiles as sharing a) a square, edge, or vertex and b) a square or hex?
Because it's easy to simply not consider them adjacent if all they share is an edge or a vertex. Making a distinction between faces and edges and vertices is more straightforward than making a distinction between two different faces. If you treat them as being just as adjacent regardless of what type of face it is, then you have bizarre distance issues no matter what, and if you treat them as not being adjacent at all, then you're kind of lying about the topology you're using.
Granted, vertex/edge borders are still annoying, just not quite so much. Hence things like diagonal flows, although I'm not sure those were a good idea to begin with.
And again, the entire thing winds up being staggered. There's simply no way to represent a two-dimensional slice of it very successfully, since the height (or any other dimension) is interlaced, in a way: Any 2D slice of nodes will look half-empty.
Oh, and I just realized another issue: It's essentially "staggered" in all dimensions, so I don't see any way to slice it up into usable cross-sections, which is what we need (z-levels).
And now my head hurts from figuring all of that out.
Thats the other problem.
Its very easy to visualize cubes stacked on each other. Its like legos. You can "see" it in your mind easily and it makes sense. We're just wired that way.
Hexes? What does a 3 dimensional hex look like anyways? How do you stack hexes? Does that even make sense?
There is no three-dimensional hex. There's no three-dimensional square either, although cubes are more similar to squares than hexagonal prisms are to hexagons.
A stack of hexagonal prisms wouldn't be that hard to visualize in-game, since every z-level would just look like a standard hex grid. The problem would be distance/travel/etc
between z-levels, and the fact that you wind up not even treating the z-axis the same as the other axes.