Less one-ways and buffs. 7sm and PB jutsus are just broken. In many cases you can only travel through one map to leave your village area (DB, KB, B3 just to name a few). In some events no matter what you do you just can't win, so why bother?
There should be more missions as well. Honestly, Rory could add a new type of mission to the third person at the mission assignment desk that rewards you with a different type of currency and gives no experience points with it's own reward set for level 60s to travel to danger zones.
New zones with it's own rewards is always good to bringing people to the DZ. Snow bandits was taken away so now there is no people moving out to DZ for that purpose.
World Bosses (WB) are done in-correctly. We got mini-bosses at takumi that will always drop ryo, but WB won't even drop you 100 ryo. There is not enough incentive for the normal folk to contest the area. Also the Monkey King is cheesed. People attack it from afar without being aggro'd unless you get 1 shotted. WB should always be on a bigger map for the damage they do.
Tanzaku should have a different type of discount for their tools or a different set of tools/weapons to use. This will move Leaf and others to bother with going out to that DZ area without being notified of someone killing a lowbie at bees.
Crafting would be a great way to bring people to the DZ. We already have blood items and psn kunai that are craftable items. More things that require specific DZ items to make will bring people out. Jobs will be another thing with similar effects. Collecting fish from a specific river, or collecting wood from a specific tree.
Missions like Blood Puppets need to be adjusted. Their sole purpose is to bring Leaf to Sand's DZ, however none will do this as it is not worth it. The mobs inside should be lessened and another room should be added to make up for this (maybe a basement). It is too tight inside for anyone to farm, especially with enemy ninja. There should be a damage adjustment too. I do not know how a WM would farm there.
These are some of the many things that could be done... Like if you agree.