I disagree. An imperfection is when it would be unbalanced. Either system can result in an unbalanced game. A good balanced game with the current system is good in my opinion and not an imperfection because it doesn't implement something that appears to resemble reality.
The system as it is now uses the time between two level ups. Only after a certain time you can increase your skill, not through practice but through knowledge. You can learn many things, but you can practice only a few. So this basically boils down to you needing to focus on a certain path and using only a limited set of skills (afterall you can only practice a few) or you can learn any skill and use the ones you think are usefull.
Either implementation results in a different game and would require a different balancing. I'm not convinced that your way would create a better gaming experience.
