Strength:
Pack Mule: In addition to its current benefits, it should also increase max stack size by 5/10/15/20/25%. The reason is that otherwise, it becomes completely obsolete later on as you start crafting pocket mods.
Perception:
Animal Tracker: Combine this with The Huntsman skill from the Fortitude tree and make it also increase the amount of materials you harvest from animals.
Infiltrator: A nearly useless perk IMO, or at best very situational, since land mines are trivial to notice and avoid, and loose boards are also not a huge issue except in a few POIs. Consider buffing this skill, such as by adding the ability to detect zombies through walls within a certain radius. That would fit the theme and purpose of the skill, and would make it useful.
Treasure Hunter: Another situational skill. Not a terrible one, but useful only when doing buried treasure quests and digging for treasure maps. Perhaps it should unlock additional (and more interesting) treasure hunt type quests at traders?
Fortitude:
The Huntsman: Remove and combine with Animal Tracker from the Perception tree. Alternatively, make it actually about fortitude, e.g. do more damage to animals (including zombie dogs/bears/birds) and receive less damage from them.
Well Insulated: Unless things like heat and cold are planned to have a much more major impact on survival, this skill is quite useless. If a total rework is not on the table, it should at least be buffed to remove severe weather effects at level 1, ALL weather effects at level 2, and provide a stat bonus at level 3 when in hot/cold weather.
Living Off the Land: A lot of people have provided feedback about this skill, but reworking it depends on an overall rebalancing of food/water as a whole.
Rule 1: Cardio: A very weak skill. At the very least, it should also improve stamina regeneration when walking, and perhaps provide an even bigger bonus to it when standing still. I don't feel strongly about this skill either way though. Might be safe to remove completely and replace with something else.
Agility:
Having Hidden Strike and From The Shadows as two separate skills doesn't make a lot of sense to me, because there aren't a lot of situations where you're sleuthing around but not killing stuff. I would rework stealth so that the bonus damage you get from stealth strikes depends on your stealth meter: the lower it is, the more damage you do, and points in the combined skill would also improve your damage (albeit indirectly). This means that, for example, if you see a sleeper and want to maximize the damage you do to it, you'd first seek out a dark part of the room, or quietly take out the light sources, which would enrich the gameplay.
Intellect:
This tree is in a good place. I think we're still missing a tier 3 baton but that's not skill related.