I admit, I choked laughing when you talk about Kapi as an example :P
But anywoo, I think a skill tree or level system needs to give you some freedom of choice to implement the way you wanna play a game that suits yourself but won't give you everything on a silver plate by the end of the journey.
The best example I've seen in a game recently is actually Shin Megami Tensei IV/Apocalypse. Each level you're given 5 points you can distrubute with 5 basic stats. Which means you can build your character towards a specific way of dealing with the battles later on (Physical build, magic build, etc ...). Also you're given 5 App points you can use to purchase "skill tree" abilities, but the catch is that you won't be able to get all of them so you need to make some sacrifices on what you think will be most suited for your playstyle (fusion-er, demon negotiator, expanding you demon slots, skill growth, etc ...).
Yeah I like those kind of systems a lot. That's kind of in Etrian Odyssey (also Atlus)
I think the thing is that most of these games that implement a progression system would have a lot of their variety ruined if they actually locked content behind the system. So they just use it as a flimsy level up mechanic rather than a system to make actual choices with. Games like this generally just shouldn't have such mechanics, because if you're game is going to be worsened by a leveling system with actual depth, you just shouldn't add the system at all.