The skills I found to be most useful, as one who mainly liked the stealth approach:
Hunter
1. Assassination Loot [Don't have to take your time looting a corpse after stealth killing someone. Useful when there are many enemies around.]
2. Chain Assassination [Good to dispatch of a close range enemy stealthily, and a longer range one afterwards when they're nearby.]
Warrior
1. Regeneration [Get this one asap. I wanted to min-max as a stealth dude, but this game forces you to go in direct confrontations quite a bit, so I was dying a lot in them before I got this upgrade, which changed everything.]
Seer
1. Smoke Screen [Also ignored to get this one for too long. When you're in trouble in combat, this makes it an easy process to evade and regenerate your health before going back in.]
2. Dawn & Dusk [Instead of waiting around for the time of day to naturally change, this just makes it a single button press. QoL upgrade.]
3. Sleep Darts [Extremely effective. Kinda OP. Long range, immediately effective.]
Do not believe in Poison Darts. They suck, especially when the enemy is near your level.