I was thinking about how could be Wesnoth remade into RTS with 3D graphics. I would like to share my thoughts. (No, I do not expect anyone starting to code this right now. Or later. It is just a thought experiment.) I would like to keep the similarity with Wesnoth where possible, but add real-time behaviour, and use advantages of 3D.
Terrain:
The map would be a 3D surface. It would be divided to polygonal areas covered by different textures, representing different terrain types. These areas would be specified in map editor.
There is a temptation to create terrains automatically by 3D height. For example places higher than 5 would automatically become hills, higher than 10 mountains, lower than 0 shallow water, lower than -5 deep water. But we would still need to separate grassland from forests and swamps. And there are exceptions, like a mountain lake (shallow water above the level of normal shallow water). So the "automatical terrain based on height" could be an optional feature in map editor, but the resulting map would have defined all terrains explicitly.
Units:
Units could have hit points, experience points, and resistances like in Wesnoth.
Movement would be real-time -- instead of "unit has X movement points per turn, and it costs Y movement points to go to this terrain" it would be like "unit moves X pixels per second on this terrain". There could be bonus/penalty for moving downhill/uphill (bonus for 3D coordinate, in % addition to terrain speed).
Number of strikes would also be defined in real-time as a number of strikes per second; or number of seconds unit stands motionless then it attacks. Ranged attacks could be really "ranged", shooting a given distance (not very far); bonus/penalty for shooting downhill/uphill. (Magical attacks would not get the downhill/uphill modification, because magical powers are not influenced by gravity.) Chance to hit -- graphically all missiles would fly directly to the attacked unit; and then some of them would display "miss" and some would display caused damage.
Villages:
Each village would have a "circle of influence" around it. If unit touches the village, and there is no enemy unit inside the circle of influence, player will gain the village. (If there are units of different teams inside the circle of influence, village does not change ownership.) Village provides healing inside of circle of influence to owner and friendly units. (If there are multiple units, total effect of healing is distributed.) Also each few seconds village generates 1 gold to its owner. -- Why bother with the circle? I want to make it possible for a melee-only unit to defend a village against an archer or two, without losing a village or healing effect just because it had to move a few pixels outside of village to get next to archer (with ranged attack), and other archer maneuvered around and touched the village. The circle of influence should be twice as large as average archer's shooting range, so that fighter has a chance to reach and kill the archer without losing village.
Abilities:
Abilities for "adjacent hexes" would also have a zone of influence. There would be a leadership zone, healing zone, etc. (With a nice addition that high level leaders and healers could have larger zone diameter.)
Charge -- when unit attacks, it changes shape, and remains in a changed chape for a few seconds. While in the changed shape, it receives double damage.
Backstab -- it would work when there is an allied unit in a reasonable angle (145-180 degrees) behing the enemy.
Slow -- applies for a given number of seconds.
Poison -- reduces hit points by one each second.
Berserk -- attacked unit must stop and cannot do anything else except attack the berserk unit. So does berserk; both units are locked to each other and combat continues until one of them dies. (If one unit has larger attack range than another, it automatically moves towards enemy. If this is not possible, the berserk effect is cancelled.) Possible addition is that units engaged in berserk combat fight with double speed (both of them; or the opponent goes double speed only if he has melee attack).
Recruited units would be unmovable for a few seconds. While unmovable, they can be attacked.
Zone of control -- when unit gets close to an enemy unit, inside of the melee attack range, and is not moving directly (145-180 degrees) away from it, its speed is reduced to a quarter. Units with skirmish ignore this, and can move next to (or directly through) enemy units, so it is not possible to stop them or surround them. For ranged units there could be a rule that if they shoot at some enemy, and other enemy stands between them, the attack is redirected to that closer enemy (but never to a closer allied unit). This would prevent them from shooting across the "zone of control".
Missing aspects of Wesnoth:
1) The rule that melee attack can be countered only by melee attack (during this turn; but can be retailated by ranged attack in another turn) is difficult to implement in RTS reasonably.
2) The rule that if unit is attacked by more units in the same turn, it has more counter-attacks, is also difficult to implement in RTS reasonably. Some units could do "area damage" around them, but that would be different.
I like your idea of using different heights for terrain. For different terrains on the same level, you can cheat a little. If plains is, say, 1.00000, then forest could be 1.00001, dirt could be 1.00002, and so on.Would placing objects on the terrain would be very hard, with slope and all? Also; does adding a third dimension improve game play? 
It sounds like a lot of hard work for little gain... (unless done REALLY well). The oomph that would be required to make the 3d graphics could be spent more wisely on 2d graphics, ditto with programming. I find sometimes a 3d ridge will give me a stunning landscape, but hide something behind it. If you can do this while adhering to the KISS rule, you might have a hit! 
Of course, if it's easy and straightforward, go for it!
