I spent more time thinking about things I would do to make the different trees more compelling.
Perception
Dead Eye
Change the secondary to give each shot a chance to ricochet, hitting a nearby zombie. Make this stack with the additional targets from The Penetrator.
Javelin Master
Roll the throw distance increase from Javelin Master into spears by default. This perk actually harms your ability to form muscle memory with spears, the throw distance should always be the same. Give Javelin Master a new secondary, chance to throw a zombie backwards and if they come into contact with a wall, hold them there momentarily.
Lock Picking
Nothing too crazy. Implement the tiered locks system daddy Bethesda uses, you can keep the random chance countdown thing. Make certain chests spawn at a guarenteed minimum with the chance to roll higher. Something like Locked Safes with Basic with a chance for Advanced. Reinforced Chests at Advanced with a chance for Master. Gun Safes also at Advanced with a higher chance for Master. Move the ability to craft lock picks to the cap stone.
Animal Tracker
Change Animal respawn rates to be different between SP and MP. I am aware this will be difficult, but recent changes to the game make this increasingly necessary. No actual changes to Animal Tracker necessary.
The Penetrator
Reduce the number of additional targets by 1 at all ranks but make it stack with Dead Eye.
Lucky Looter
Each rank gives a static +2 Loot Stage along with the percentage.
Treasure Hunter
Make unperked digging take 12 blocks and this perk reduce it to 10, 7 and 5 respectively.
Strength
Boomstick
Move to Fortitude Tree. It's short range which lends itself to the up close and personal nature of Fortitude and not heavy enough to think it belongs with Strength.
Heavy Armor
Move to Fortitude Tree
New Perk: Moving Day
Give the ability to pick up certain unclaimed decoration blocks by long pressing E. Each rank adds more (heavier looking) decoration blocks.
Pack Mule
Change to increase mobility when it's less than 100 by 3% per point. This makes it useful at all stages of the game.
Master Chef
Move to Intelligence
Fortitude
Machine Gunner
Move to Strength Tree. These are heavy weapons you'd need a lot of strength to wield. Plus it offsets some of the large amount of power being moved out of the Strength Tree.
The Huntsman
Benefited by the same change as Animal Tracker.
Living off the Land
Craft all seeds at rank 1.
Harvest 2 at rank 2.
Healing Factor
Change Regen scaling to: 60, 50, 40, 30, 20. This is too strong at higher ranks and a little too weak at lower ranks currently. Even with this, the highest rank is still triple the strength of the lowest rank and it is still the strongest scaling perk in the game.
Iron Gut
Reduces passive food and drink depletion rather than active.
Rule 1: Cardio
Move to Agility and make it reduce food consumption from running as well.
Agility
Archery
Gives a chance to inflict bleeds at higher ranks.
New Perk: Deft Fingers
Take all reload speed boosts from other perks and put them here instead.
Light Armor
Change bonuses to give a chance to dodge attacks per slot of Unarmored or Light Armor worn.
Hidden Strike
Add an increasing chance to land sneak attack damage during the night while crouching in combat.
From the Shadows
Add a decrease to the range from surface horde can detect you and the AI director can detect your heatmap.
Intellect
Electrocutioner
Move its secondary effect to Nerd Tats and the Nerd Tats effect to here. Stun Batons need their 3 tier treatment as well, or a general rebalancing. They are in a very bad place right now.
Charismatic Nature
Move Rank 2 to Rank 1.
Move Rank 3 to Rank 2.
Rank 3: For players in range, grants an additional temporary point in Healing Factor and Sexy Trex. Create hidden extra ranks for these perks unatainable without Charismatic Nature.
Healing Factor 6: 10 Seconds
Sexy Trex 5: Tool and weapon stamina usage reduced by 30%, Power Attacks still 50%. Refunds 35 stamina on kills.