While a character that chooses to train a great number of skills may be very versatile, it is not nearly as good or specialized as someone who dedicated all his time to train in a small set of skills.
Think of it this way, you might become a fighter with good spellcasting abilities, martial arts knowledge, stealth and thieving skills, yet you are not as great as a pure fighter when it comes at melee combat, or as a mage when it comes to spellcasting, and so on.
If you played Baldur\'s Gate 2 (I know, it uses a class and level based system, but I think it helps to get the point across) you will remember a multi-class, the Fighter/Thief/Mage. They are capable of doing almost anything, but not at a very high level.
As Kendaro said, you are a jack of all trades but a master of none. If you dedicate your time to study a wide range of skills, you will never get to master them all (unless you play 24 hours a day the seven days of the week
)
It is a hard task for the devs to balance all the skills, due to the almost infinite amount of possible combinations. It is much easier to do so in a class based system. The trick will be to limit in one way or another what someone can do when combining two skills.
So, for examble, if backstabbing is in the game, nobody should constantly backstab an enemy when under the effect of invisibility. Invisiblity can be a very unbalancing spell if it isn\'t well implemented, as well as those that do not allow to defend yourself, such as paralysation or petrify (nothing worse than being forced to stand there and be killed).
