The problem here is not the a la carte option. The problem is that some skills are just plain better than others. That is what needs to be fixed.
I have seen people claim that Profession Lore and Heraldry Lore (I really dislike the latter name and hope it is changed) are worthless and traps. Granted certain professions might be harder than others to justify. However, for many campaigns, Heraldry Lore and many profession lores are very valuable skills and can be more important than many other skills or even combat ability.