Skills tier list. It's ordered, so the one on top of each tier is a little better than the one below it.
Note that skills are shared between both protagonist characters. This is important because the Grapple skill is useless for the female protagonist, but leveling up while using her will still apply the level to the male protagonist.
S Tier (Always extremely important; invest as soon as possible)
- Harvest - The premier skill in the game. Upgrading Harvest allows you to get resources far more efficiently. This includes everything from wood, to ores, to berries, to flowers. They are all multiplied by a considerable factor. It does not apply to combat-related drops like animals or monsters, though. By attaining a high Harvest level early in the game, you will save yourself a tremendous amount of menial labor.
- Self-healing - Heals you when out of combat, allowing you to recover quickly between combat and also save on precious herbs. Your self-healing skill seems to also apply to companions who are following you. I believe that you only heal when your hunger level is above zero, which also applies to your companions, so make sure to feed them if you notice their health is not recovering.
A Tier (Often important; situationally very important)
- Smash - Deal more damage with power attacks (press F). The decapitation bonus isn't very useful, but the raw damage output allows you to one-shot a lot of enemies. The Smash skill is not quite as important as the strength stat, but the damage multiplier helps a lot. Eventually you will only want to use power attacks, not only because of the multiplier, but because both normal attacks and power attacks only damage your weapon by 1 point.
- Carry - Allows you to carry more downed NPCs, both human and non-human. Higher levels allow you to fast travel with more of them as well. If you are looking to build a larger settlement, this will be essential. I used skeleton guards to defend my city and without a high Carry level I would have needed to delve into the dungeon dozens of times.
B Tier (Often somewhat useful; situationally important)
- Grapple - When you attempt to rape via grapple (press R), the Grapple skill will increase the timer and reduce the amount of clicking you have to do. This is mostly useful if you rape a lot of NPCs. With a low Grapple skill, you may have trouble raping even friendly/tamed NPCs, which can be annoying. With a high Grapple skill, difficult female opponents like Large Female Native become trivial as you can press R on them and completely neuter them.
- Leader - Increases the number of companions who can follow you. It is a bit misleading, because the number is not a number of companions. It is a "size" value. Some animals have a "size" of 1. But larger creatures like the werewolf take up a lot of "size value points", in the case of the werewolf I believe 5. If you want to have powerful companions like werewolf or bigfoot, you'll need to level it up. It is also a useful skill for moving multiple people around without needing to rely on the Carry skill.
C Tier (Often mediocre; situationally somewhat useful)
- Construction - On the surface, the Construction skill seems to only increase the building radius. This isn't very useful, since you're probably not going to be building that far away to begin with. However, it has a hidden effect. By increasing your Construction skill you can repair destroyed objects more quickly, like walls. Later in the game, native scout patrols will absolutely decimate your walls, and without a higher Construction skill, it can be tedious. However, this can be mostly mitigated by assigning NPCs to the Repair task, making Construction generally mediocre.
- Observation - Allows you to see various NPC stats like HP, faint, age, and personality. Seeing HP and faint is not as useful as it may first seem, since by the time you should level up Observation, you are probably killing everything in 4 or 5 hits at most Also, the combat is so simple that even if you knew the enemy only had one hit left, would it change your behavior at all? I doubt it. However, seeing the age and personality of an NPC is super useful. If you wish to age up or age down characters using growth or rejuvenation potions, seeing the actual number will help you gauge the amount of ingredients you need. With personality, this is incredibly situational, but if you want male NPCs to rape female NPCs you will need to find the correct personality type matchups.
D Tier (Often useless; situationally mediocre)
- Patience - Reduces the rate at which you lose hunger and thirst. Food is not really a problem in the game at all if you casually collect it as you explore. Neither is thirst with near-unlimited access to berries (shift + click to consume 10 at once). This skill is really just a worse version of Harvest, but it may be worth sinking some points into later when you have points to spare. The depleting food and thirst bars can be tedious when fast traveling around a lot, so Patience curbs it a bit. Even if it relieves a bit of tedium, I can still barely notice the difference between level 0 and level 5.
- Persuasive - Multiplies the effects of persuasive actions (hold Q), both positive and negative. This is somewhat useful if you don't want to use the speed up feature (SHIFT + .). It just saves time in a few uncommon situations where affection adjustment is needed. Players who don't like to rape and prefer romance will probably find Persuasive to be more valuable.
F Tier (Almost always useless)
- Swim - A nice skill in theory that may become useful later in the game's development. As of right now, though, the best way to cross ocean water is to use the raft. There are no wide rivers that take more than 7 or 8 seconds to cross at the lowest Swim level. A very obscure use of Swim is that when using the raft at high speed-up levels (SHIFT + .), the game will sometimes force you off the raft. If your Swim level is 0, you may drown if the game is sped up fast. At a high Swim level, you will survive long enough to get back on the raft. If you don't use the speed-up feature at all, the Swim skill is almost completely useless.
- Stomach - Reduces the probability of food poisoning, all the way to 0%. I have never needed to eat raw food. Cooking is instant and easy at the bonfire which is provided to you at the beginning of the game. There aren't even that many foods which yield food poisoning to begin with, the only useful one being raw meats. This should be the last skill you level up.