The problem is this: if WotC explicitly gives us the option to pick skills and feats a la carte, then immediately picking them a la carte becomes the norm. Any player with even a passing interest in character optimization will always hand-pick his skills and feats. Want to make a character who used to be a blacksmith? Well, pick the interesting and potentially useful Item Crafting Trait, but drop the crappy Local Lore and Professional Lore for something better. You're just as legit a blacksmith, but your skills are way better. You'd be crazy not to do it, as long as character effectiveness matters even a little in your group.
There's a way to have both, and to have both be viable options, even in the same group.
The way you do it is to first set out the skills and feats separately, and balanced in their own right.
Then, package them up into bundles (specialities and backgrounds), where the "blacksmith" bundle has that Item Crafting trait and Professional Lore skill.
But here's the key thing: provide a (small) "price break" for accepting the bundle, but don't allow any substitutions or alterations from the bundle - you either take it as-is, or not at all.
And so, switching out that Professional Lore for "something more useful" is a no-no - if you want to get rid of that, then you
have to choose a la carte... and that means paying more for the individual bits.
(The reason you can do this and have it remain balanced is precisely because the bundles are non-optimised. The char-op people will thus have numerically 'weaker' characters, but can be assumed to have gained more bang for their buck, whether due to system mastery, or because they've consulted the boards, or what-have-you.)
It is, however, important that the designers are conscious of this, and that they don't proceed to create bundles for every conceivable combination of skills and feats! Providing price breaks like this only works if the bundles are reasonably but not perfectly optimised - if you can just select "a bundle of what I would have chosen anyway", then it's potentially a problem.