Instead of skills only progressing by skill points, I think a system where you level up skills based on doing the action sounds better. I have spent hours mining for Ancient Tech, and I felt I did not gain anything from this. Doing that much mining and having a tool level up maybe a few times feels more like I did not waste my time.
First, the skills and skill points that exist now will stay the same.
The new thing will be item skills. For example, you must mine with the stone hammer ___ amount of times until the next level unlocks. The next level could give faster speed, higher durability, etc. After a few levels later, you then unlock the ability to craft the next tier hammer. You must spend one skill point to learn this.
This is how I would redo some of the skill trees.
Core
-Stays the same(5 skills points for each)
Attributes
1. Vitality: Increased by taking damage from enemies
2. Power: Increased by doing damage.
3. Control: Increased by placing blocks and throwing.
4. Dexterity: Increased by placing blocks and mining.
5. Agility: Increased by dodging attacks and scoring critical hits.
6. Intelligence: Increased by healing and crafting new stations.
7. Luck: Increased by finding rare materials and looting.
8. Energy: Increased by sprinting and jumping for long distances.
Each of these has 20 ranks. Each rank requires 2 skill point and a high enough level in that attribute. Do the above action to level the attributes.
Tools
Each tool has a separate skill path. Each new rank requires 2 skill point and a high enough level in that tool.
Each tool follows the same path.
Rank 1: Stone Tool
Rank 2: Tool swings ___% faster.
Rank 3: Tool has ___% more durability
Rank 4: Next tier tool unlocked
Rank 5: Tool swings ___%faster
Rank 6: Tool has ___% more durability
Rank 7: Next tier tool unlocked
etc
These level up by using and creating the tool.
Crafting
Similar to the tools in terms of how to unlock ranks. These are split into: Machine, Engine, Prop, Item, Block, Decoration.
Rank 1: Item
Rank 2: Item crafts __% faster
Rank 3: Item has a ___% chance of not using all materials required
Rank 4: Next tier recipe unlocked
Rank 5: Item crafts ___% faster
Rank 6: Item has a ___% chance of not using all materials required
Rank 7: Next tier recipe unlocked
etc
These level up by using the station or creating the item.