I really like the Job Point system itself, however in my opinion the main problem is the need to kill large amounts of monsters at a fast pace in order to gain decent CP, so the changes should be aimed towards making individual fights far more significant while discouraging AoE capable jobs from hogging large amounts of mobs. Making it so continuous chains provide the best CP per hour so areas can accommodate more players and AoE jobs can switch to smaller scale tactics without losing their premium CP gain.

The kind of changes I would personally like to see would probably be something like this:

1) Nerf AoE killing. Make it so killing/holding more than 3 mobs at the same time is pointless by making the 2nd mob give only 50% CP and the 3rd only 25% CP, with no gain for additional kills by the party. While also making it so there is a 3 second delay to be able to gain CP again or trigger following chain extensions.
2) Increase the HP of all CP capable mobs to at least 300% of the current value. So individual fights take longer.
3) Double the base CP and increase the chain CP bonus amount so we can obtain triple (chain 10) to quadruple (chain 20) CP.
4) Reduce the recast of Capacity ring to 5 minutes and give it 10 charges.