The system is fine but it does need some rebalancing.
I think treasure hunter and the lockpicking perk could easily be merged as they are both far too niche to really be playstyles. I think forge and workbench need to be basic recipes that are always known, the limiter should be resources not luck or just picking int. I think salvaging and grease monkey should be merged and put in the int tree, as crafting skills feel bad if that's all they offer and cost reduction for something that you will likely only ever craft once feels bad.
I think every branch needs one harvesting skill, int can have salvaging, strength mining, agi should have pelting, endurance has LotL and perception I guess has lucky looter. Less lucrative harvesting skills should get some other bonuses too like randomly harvesting a valuable item that you can sell at a trader (thinking of pelting specifically, you could harvest trophy heads that sell for good coin at the traders since bones and leather have a limited amount of uses)