The hexes aren't the problem, the 3D implementation is the problem. You constantly have to rotate the map to either find the selected object or figure out which hex you need to click to select it. Trying to get around this by switching to the 2D overhead map doesn't help, because the scale and orientation changes between views, so you've got to scroll around and search for the object again every time you switch between the two. The flags and status icons are sized such that you can either set them to be readable, or to not block other labels, but not both.
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Well said. This was the most frustating thing I noticed when I began playing around with the demo. Very quickly I decided: "This is far more trouble than it's worth."