Hey, I'm not a lawyer, tax lawyer or otherwise. But, as far as I can tell, Apple has been following the (Irish) law. Quite openly. I don't see the fraud or deception. Of course, I only know what I read in the New York Times. But, if the law and regulations need to be changed, change them.
More generally, if the EU does not want for individual countries to compete with each other via tax treatment, it needs to set common tax laws across the EU. I think with situations like the current one, and, the banking crises (the "PIGS", etc.), I think it is apparent that the EU's "common market" has a lot of internal inconsistencies. Didn't matter much back when in every country, there was agriculture, manufacturing, and mostly local services. Now that a large part of the economy of every country depends on services that can be provided in part from abroad, all those inconsistencies are a huge problem.
The U.S. has a similar problem -- states are competing with each other on the basis of favorable tax treatment. Every state offers itself as a location for businesses to incorporate under state law, and, at tax time, it makes a difference. There goes your "level playing field". It didn't matter that much in the past, but, in the Internet Age, it matters a lot.
I think a common set of rules for corporate taxation should be at the center of the WTO. When the commodity flowing across borders is information, tariffs become insignificant compared to corporate taxes.