Limiting skill-based progression?

Hello, everyone. Nice to meet you. Some recent reading reminded me of a problem with skill-based rule systems: namely that it's quite possible for a character to become the best at everything if the game goes on long enough. What would be a good solution to prevent that without feeling like a forced, arbitrary limitation?

Note, the question relies on the assumption that the use of a class-based system has already been considered and rejected for the author's hypothetical project.

(And yes, the question is purely hypothetical. I'm not working on any RPG right now.)