Well... it depends what you mean. For the purposes of argument, I shall assume you are referring to ice-cream.
The store-bought chocolate is indeed typically far from nicer than vanilla. However, using vanilla, chocolate can be created from it, or can be augmented into it, in such a way that it is better. There are many ways to do this... mixing with Milo (or whatever the international equivalent is, I don't know how widespread it is), chocolate flakes, those hard-setting toppings...
That said, my favourite ice-cream creations are vanilla mixed with milk powder (try it, tastes very nice) and vanilla mixed with a cereal we have here called Special-K (gotta try something like it, quite unique texture).
One could argue that simply because vanilla can be used as a base for a far greater number of creations, including chocolate itself, that vanilla is superior.
I do.