I have 30 points in Intelligence, but I can't really see the purpose of it. Does it do anything or is it there just to waste skill points?
It increases experience gained from an enemy.
This can be seen in combat.js which shows:
data.experience.value += exp_per_enemy() * data.intelligence.value
meaning experience gained scales with intelligence.
Note: It does not increase exp from quantum boxes - the file lootdrops.js does not contain "intelligence" at all.