1) Map Rotation - its super nice in Fantasy General to be able to rotate the map as needed to better see around. One of the whole advantages of a 3-D map is the ability to view it from different orientations.
2) Unit Movement Path Selection - Being able to specify a units movement path with ctrl-click to plot out a route. Its very frustrating when you know there is an enemy unit in the fog of war but you can't direct your panzer to move around it.
3) Mini-Map Display/Hide Toggle - There are options to display or hide all the other UI elements, I'm not sure why we can't do this with the mini-map. It takes up a lot of screen space, even fully downsized. I find it a cluttered and ugly mess and rarely use it. Funny enough I find the mini-map in Fantasy General really helpful and so do use it there, it is very clear and highlights all the points of interest.
4) Left click to Select, Right click to take Action - Panzer Corps using left mouse click for everything feels very natural for me and leads to frequent mis-clicks. It would be nice if this were an option in the key bindings.
Edit one more 5) When your units get award bonuses during the AI turn. The award popup covers much of the screen but the combats continue behind it. Combat should pause until you dismiss the award notification. Currently I don't have time to read the popup while I have to hurry to get rid of it so I don't miss the AI combat round.

I'm not sure if these have already been discussed of if I'm the only one with these concerns. But thought I would throw this out there.