I think the main problem by most games in the past was that developers inserted a lot of skills/talents/traits but often ended up neglecting most of them in the gameplay that many got quite useless or even redundant.
Some of them might not thought about that as others might had plans but had to cut corners because of budget issues as time is ever a big fiend of game makers, especially when you are not independent.
another big point is of course how central armed conflicts are in most games so that most people tend naturally to focus their points on everything which let them survive.
At the end it lies mainly in the hands of the developers if they take in a later production phase a re-look over their skills and make adaptions to the path the game took with time and cut a skill which looked good at first, maybe add another which fits better as long at least the majority of skills can have somehow some influence in the game.
In a paper game we made you could also pick quirks which gave players a few more points in skills but also added aspects to their characters which could be a more or less serious disadvantage at times. At first they were not too thrilled but realized quickly how much fun actually those quirks could be as it added depth (and realism as their hero was not perfect) and added interaction hooks between players.
