I haven't thought too much about it. Most fun might be if the weapon "pickups" were in the original order. It would make the first maps (8, 7, 6, 5) bloody hard with the weapons of the 1,2,3,... maps.
But easier would be to backpackhack strip the player and provide "the weapons you would normally have here" at the spawnpoint.
So far I am playing with the route, changed some targets, trying to re-use the existing things as much as possible. I have to think of something smart to disallow the player to just drop from the top floors into the lower areas (at least a bit). Here is a very early "conceptual" build, maybe it shows a bit of my vision about the backwards map: http://www.quaddicted.com/temp/e2m3_spirit_20090921.bsp
Stupid fucking QuArK does not let me edit textures when I use it with Wine. Bah.