Nah, I’ll go with classic DnD/Pathfinder skill points, though simplified to make them less overwhelming.
I see stats, in games like these, as a easy way to keep tabs on previous “abstract” choices. I.e. you might have eight points in the game where a player can demonstrate their skills of persuasion… It’s much easier to say is persuasion > 4 in code than it is to say: if 4 of the 8 choices. They’re used as a sort of framework to guide both the author and writer through a “route” of the game, and they do help with planning in that respect.
Unless you’re going for a full RPG type experience, or some other more game-like design (where stats become interesting), I’d always try to avoid heavy usage due to the reasons mentioned above.
To answer your question though: I plan to make the only restrictions on future choices be old choices which ironically, is no different from stats, if you think about it. At some point you need to limit the scope, and however you do that, the end result is going to be similar. It’s only the perspective that’ll change. For me it feels more organic to miss out on options because I made actual previous tangible choices (e.g. betrayed the king, so don’t get knighted), rather than winning a fight because I remembered to spend my free time in the sparring ring (fighting+10).
All that said, I honestly think the most important thing to do is just ensure that every playthrough is enjoyable. Stats or no, don’t punish people, just give them alternatives. Make them want to try the other routes, even if that means “failing”. Maybe you lose the fight, but meet a cool new character, and get an extra scene because of it. Like in my previous example, betray the king, but get a shedload of coin and your own magical kingdom. 
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