Also if you can make it so bots can't see through shapes and try to get to a bot on the other side whould be nice. Even if that function is not checked in the topography they still see through the shapes.
I cannot reproduce this. Currently, bots should see nothing when they look at a shape - not the shape itself and not the bots behind it - when the "Bots can see through shapes" checkbox is unchecked.
If you have a sim which demonstrates this, I would be very intrested in seeing it.
And it whould also be nice if ALL settings in the topography are saved in the sim.
Agreed, in part. I will be adding such to saved sims in future versions, at least those settings directly related to the operation of the sim such as shape drift settings. One could make an argument however, that options of a purely visual nature which do not impact the sim but rather are there purely for the viewing convience of the human should not be saved in the sim file. For example, the setting for disabling the graphic display or for disabling poff shots. I would add to this list the settings for viewing shot impact dots, resource gugages, movement vectors, the vision thingy and so on. Such settings have no impact on the execution of the sim (other than speed). They are there for the human observer.
If I load your sim, should all my non-sim settings change to reflect those in the saved sim file? I'm not sure that they should. I will indeed add those which do impact sims directly, but I'd be interested in other opinions on the rest.