I kind of agree, but I'm not an EU citizen and don't have any say in EU laws, so whatever :) If I were Apple, I would be a little miffed at this situation, though. It certainly makes me question whether or not I want to ever expand into the EU. But tax laws are too damn complicated in most other countries too. so maybe just budget for government incompetence?
The EU isn't going to get the taxes (certainly not the vast majority of them). They just ruled that it isn't OK for Apple to have been given this tax break via specific accounting rules. It's Ireland that gets the windfall, whether it wants it or not.
Other countries in the EU, however, can sue ireland for taxes they missed out on. Which is probably what will happen. The money will be divided up over many countries.
On what basis exactly? Income is taxed where the company (Apple subsidiary) is headquartered, so they would have to prove Apple would have chosen a different country, which is not going to happen.