The biggest downfall I've seen so far discussed about Star Wars Saga-like skills is that all of them consistently increase, whether trained in them or not. Conan the level 20 barbarian will know as much about spellcraft as the level 1 wizard who spent all of his formative years in the academy of magic. Also, the negative connotation is that you won't have a character who ISN'T skilled in any skill whatsoever - the tweaking and customization that some players enjoyed would be gone.
The first point I can see, but to me the more realistic is that you're going to know a little something about everything if you're a super-bad level 20 adventurer. James Bond knows a bit about everything, from cooking to computer hacking, and the level 20 adventurer is the fantasy equivalent. Conan doesn't know that the shimmering wall is a wall of force, he instead knows that it's just like the wall that Pelias dispelled when fighting "that stygian wizard that one time", and Pelias called it a "wall of force."
The second point has more bite, because it directly cuts into player fun. If there are enough players out there who want that customization, I think it would behoove WotC to have at least an easy optional rule to allow for it -- and personally, I think there are enough that they really should think about this. Not everyone wants that Conan with the +10 spellcraft, and telling them, "just don't use it," is kind of like telling a cleric not to use his spontaneous cure spells when the party needs it.