Melvor Idle

Melvor Idle takes the twenty-plus interlocking skills that make RuneScape's progression interesting and removes the part where you have to click a tree for nine hours. What is left is the actual design, the dependency graph between gathering, processing and combat, where training one skill funds another and the optimal route through them is a genuine puzzle.

It is not a shallow clicker. Combat has real gear and prayer systems, there is a full agility and slayer implementation, and the expansions add mastery layers that keep the optimisation problem live for hundreds of hours. Jagex publishes it, which is unusually gracious given the source. There is a free browser version, and the full game is a one-off purchase with no other monetisation.