Here's a simple idea to make player bounties work:
Bring back daily/weekly Illum to bring people to the planet. When you enter pvp area on Illum you may get a bounty from terminal located in your base. The terminal gives you a bounty on specific player from other faction who is currently in the area(it's chosen at random to avoid kill trading) . To complete the bounty you need to kill the player. If the player leaves the area(by joining a WZ/logging out or just leaving) you lose the bounty, but you get assigned to another player automatically. If you leave the area you automatically fail the bounty too.
Same system may be implemented on all planets, but with level restrictions. Players above certain level can't get bounties on players so there would not be roaming 50+ players on low level planets killing lowbies. The bounty could specify the location where the player was seen too(not direct location though) to make the hunt a bit more interesting.
On PvE servers only flagged players would be chosen for bounties - so yea PvE servers would be kind of screwed, but if you wanted to pvp you shouldn't have roll on PvE server(same with the opposite if you didn't want to PvP you shouldn't roll on PvP server).