[quote:15e9geye]Edit:
Another way that might work, could be if you could create obstacle maps kind of like you would a layer. So as you add them you would be able to choose which obstacle map an object would use in the properties panel just like with layers. And maybe be able to switch them around during runtime and so on. But don't know If that would cause memory problems as well.
I think this should be enough. For instance on isometric game where you would have multiple floors kind of like old X-Com games. When changing floor you could switch obstacle map to "Floor2" and maybe for add obstacle you would have new setting for what obstacle map you would like to add that.
Would it still be too much if instead of using own map for every instance you would use predefined amount? For instance on this RTS example there would be 2 (air units probably don't need one), on old X-com there is 4 and on X-Com: Apocalypse there is 9 etc.