The following ideas are in reference to the current bounty/kill system, and are not meant to all be worked together, but rather are separate ideas to rework various problems/situations with the current system. The current state of things are Safe Zones do not count for mission kills, bounty collection, or your kill count. The thought process behind this (at least in my own eyes) should be- When you get a kill in a Safe Zone, it is still a kill. it should be counting for missions as well as your kill count as a death is still on your hands. Bounty typically would be harder to claim in a village due to the resistance you would face from the village while you're trying to escape with the body. (In the Naruto verse, you need a corpse to claim a bounty on someone's head). So here are some ideas-
1) Bounty Collection rework ideas-
a) Dropped item/headband collection. This is fairly simple and straightforward idea. Create an item that drops on death worth the amount of ryo a normal bounty collection would. You would need to collect said item and bring it to the bounty house to collect the bounty. The items could be locked to opposing villages, so if you were in leaf you would be unable to collect a leaf bounty, and the bounty would not be reduced from the ninja who dropped it until it was collected(or the player attempted to log out to avoid it). It can also just be destroyed by the village it came from to negate the collection.
b) Raid Point bounty Modifier. The idea behind this is fairly simple, if you have raid points, have it affect your bounty loss. This will give more reason for villages to go after points, rather than just for PvE. For example, if Leaf has a -5% bonus, and Sand has a 20% bonus, have that reflect in bounty collection when you die.
For breakdown sake- Leaf has -5%, when they die in a DZ, they lose 5% more bounty than they would with a 0 bonus. Ie if you had 200 bounty and died, instead of losing the normal 100 bounty, you would lose 105. Sand has a 20% bonus, so when they die with a 200 bounty, instead of losing the typical 100 bounty, they would lose 80. I think this would stress raid point importance to the vast majority of PvPers in Nin.
2)Mission Kills/Kill Count idea-
a) Simple and straightforward. Make kills count in safe zones. No matter where you are, a kill is a kill. It should be counting regardless of your position. I won't go into detail too much as I feel this one is a no brainer.