Using the Z axis to attack a SB is obviously cheating because if it was just "part of the game" then a TEC or Advent SB would be able to react to Z axis threats.
For everything else I don't think the problem is so much that there is a Z axis, but that it is a poorly designed one and obviously an afterthought for the developers. Think about it, gravity wells are 2D, so is every map except randomly generated ones. Only in random maps will there be "Planet stacking" as I call it and it is universally annoying to have to deal with. If it can't be done correctly then don't do it. But that isn't to say don't do it, just correctly. 3D gravity wells, 3D maps, 3D SB weapons and a making a tutorial to help new people grasp the idea before they get destroyed by in on ICO.