Thanks for your answers
1) The campaign system will likely be different. Several ideas have been proposed but it probably will not be the same type of strategic map that we have now. This really hasn't been solidified enough to give information yet.
mmmmh I'm afraid of this

(I find the actual stratmap one of the major evolution of the CC series so far)
2) Buildings (I assume this is what you mean) will probably still be somewhat abstract, with infantry able to enter or leave by going through the wall instead of using doors and window
curious to see how the game engine will use the 3D objects then. the possibility to go through the wall have always bother me for unit entering a multiple floors building.
3) My current plan is to have a map editor where the player 'paints' a ground texture onto the map (like grass) which both colors the ground and codes it at the same time. You then add 3D objects like buildings, trees, walls, etc. Stone walls and wood fences would have both separate 3D models and separate textures.
Will the stone wall still offer better protection than the wood one? Will each 3D objects still have protection and cover values? Hope we will be able to import our own models! Will the buildings be destructible?
4) I assume you mean floors within a building -- what I want to do is allow the player to control what floor an infantry unit is on by being able to order them to go up/down floors within a building. This does introduce some UI issues (how do you tell what floor they're on? How do you order them to go up/down? How do you select units when one is directly above another in the same building, etc) but I think we'll be able to solve them.
yes a lot of problems to solve! good luck!

and don't forget the hand to hand battles in buildings with multiple floors : one challenge more!