Whole Foods Market, the Academy of Chocolate, and other superficially quality focused organizations have all picked an unlikely whipping boy to highlight poor quality and artificiality... vanillin.
What is vanillin? It is the chemical responsible for the dominate flavor note in vanilla and it's what makes many barrel-aged spirits, wines, and vinegars "smoother" with time. In fact, a fun trick is to turn rotgut scotch into fancy scotch by the addition of a drop or so of vanillin (a fact that doesn't overwhelm scotch makers with joy). The final product will have the brightness of a young spirt and the smoothness of an aged spirit... typically mutually exclusive results excepting only masterpieces of the industry.
I understand that the larger, lower quality, industrial chocolate makers and chocolatiers often use vanillin because it is cheaper than vanilla. These same entities also use white sugar, yet that doesn't preclude it from artisan work. I also understand that typically vanilla is produced from paper byproducts, but this atypical food extraction, artificial creation doesn't change the fact that it is naturally occurring and vanillin from the finest vanilla beans in the world is chemically identical to vanillin made in the lab.
I believe that vanillin should be re-examined, particularly for use with finer chocolates, where only the smoothing effect of the vanillin is required and the many other components of vanilla are either lost or conflict. Also vanillin could be an invaluable tool to chocolatiers working with wines and spirits, where an inferior alcohol can be artificially aged to the benefit of the chocolatier and the customer in terms of superior quality at reduced cost. In these instances again, actually vanilla may clash with the other subtle notes of these younger alcohols.
I would no sooner suggest vanillin as a suitable replacement for vanilla than I would truffle oil (2,4-dithiapentane) for fresh truffles, but this does not mean that no other uses exist.
So seriously, give vanillin a chance, just remember, it's a unique ingredient with unique uses that could (and dare I say should) be in the stock of every fine chocolatier, not just cheap vanilla. It's only unfortunate that it will take a large effort to sway consumer opinion on this matter.