Balancing is not an issue here. I can't understand. You have to balance sides, right, gameplay exploits, fine, but if you give the exact same thing to every player, an universal rule, why does that have to break anything? There is some cases where this don't apply, yes, but in that particular case, z-axis won't break the game at all.
Then again, I agree your point about exponensial issues with options, but that doesn't mean you have to restrict yourself too much.
Every game have multiple rules for multiplayer...
And too late for major changes? WTF? Everything is already there! The only thing missing is z-axis structure placement! (And since the z-axis exist, it's only a interface issue...)
I've shown the game to many friends (so they could preorder it and play against me

).. all of them (5) replied me the same thing: "Hum, ok, so its flatter than starcraft then... I'll pass."
Please please please... I beg anyone @ IC.