I think the answer is limits, let the player build as he wishes but not let him be excelent at everything, in other words stricter level caps, in a way that at max level you can be a heavy armor wizard if you want, but you can't be a heavy armor wizard that is also master on melee and archery and stealth. Either less level or less points to asign for each level is the answer, so you can't be so good at everything.
Fallout is the same, at max level you are 100 in several skills, and in the rest you are 80, and in the SPECIAL you can have several at 10 just through special perks gained throug other means.