I know that free roaming mobs has always been an awesome idea for any mmo, however I think this idea has plagued Xsyon from the very beginning.
I think a lot of extra time and resources goes into constantly trying to fix and refix the way mobs roam, breed etc and trying to keep enough mobs in every area of the game to keep people happy.
1. Keep zombies tied to the totems they spawn at, the larger the tribe zone they are coming from the more zombies there should be spawning.
2. Place mob spawns around the game world, place different types of mobs in different areas. (for example don't put bears in every zone, keep them in a specific part of the map, like only in the NW or only in the South, etc) Keep them "leashed" to their spawn unless they are attacked or someone enters their spawn area. (same goes for zombies, they don't attack unless you get within range)
Now, since you have the code already for free roaming mobs you can put in a twist that no other mmo has. Put the mobs that spawn in on a timer, like 7 days - if they haven't been killed within 7 days their "leash" to the mob spawn is released and they will free roam until killed. The spawn that they came from will not reproduce more mobs for 7 days or until the mobs from that spawn have been killed. (the 7 day timer could be lowered as more people start playing the game)
You could take out breeding or customize it so that breeding is based on the amount of the current animal population when a check is performed, if their are to many animals then no breeding is allowed. If there are too few animals then breeding is allowed and more mobs spawn in at their spawn location.
One of the main things this will do is create PVP hotspots, people don't like spending hours hunting for mobs just to end the night without finding any. Or spend hours looking for animals just to find one that kills you and sends you back across the map to your totem.
It was said that green mist pockets of gas were left in the new areas, this could be where the "mutants" are spawned from and they could be free roaming only, also mobs that do break their leash after not being killed soon enough would mutate as normal when they wonder into the green mist.
This is one step towards giving exploration some meaning, you'll want to go out and find those abandoned totems and to also find the best mob spawns.