Can't talk about this without giving props to 'So I'm a Spider, So What?' and how it handles things. The MC's entire existence is basically a skill tree nightmare—or playground, depending on your perspective. She's literally a monster evolving through a system, unlocking crazy abilities like parallel minds and taboo. The interface itself is a huge part of the plot, which feels fresh.
You also get 'Kumo Desu ga, Nani ka?' where the skill tree isn't just a menu; it's a core mechanic that drives both her survival and the world's underlying logic. It gets deeply intertwined with the lore later on, which I find more satisfying than a simple stat screen. Others might point to 'The Rising of the Shield Hero' for its weapon-based progression, but that feels more like a single, branching path than a sprawling tree. The spider series really leans into the 'tree' metaphor, with prerequisites and weird, costly evolutions.
I stumbled on a lesser-known one recently, 'I Grow Stronger By Eating!' where the protagonist absorbs traits from monsters, creating a kind of organic, customizable skill set that mimics a tree structure. It's a bit more gruesome, but the build-crafting potential is huge for theory-crafting fans.