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.
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?
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.
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.
This tree is in a good place. I think we're still missing a tier 3 baton but that's not skill related.