I like the 3D map.
I just use the cloth one to find goodies, quest objectives or my far away units. If these would be better signalized, it would be perfect. And to whom belongs a unit should be more obvious too.
Same here - I play on the 3-D map but either zoom out or switch it off for a moment to find quest objectives (that nice BRIGHT gold icon is nice)
I think some things that could be more apparent on the 3-D map:
-Icon of the nation's crest a unit belongs too (i.e. a stack from Yithril will have their nation's crest under the stack) and somewhere on the unit card when you mouse over the piece on the map (maybe as the background off the text portion of the card)
-Some of the goodie huts are hard to tell from just random terrain doodads.
-Wild Wheat is flapping hard to see on the 3-D map, make it taller or something. Fertile Ground could use some more green-ness or something. If there's some grass in the middle of a barren wasteland, it would stand the flap out big time.
-Quest objectives should shimmer or have that gold cloth map icon under them.