The EU Commission is suggesting that Apple should have been paying more tax and that Ireland aided them in achieving that outcome. If Apple was compliant with legislation/regulation at the time they should not be thrown under the bus of inappropriate transfer pricing practices and being a poor global (corporate) citizen.
It has been noted by many in the tax industry, that every company (large and small) seeks ways to (legally) minimize their taxation outlay. If Apple adopted transfer pricing strategies that were in keeping with the law at the time then they should not be taken to task.
The G20 approach to a multi-lateral rather than a bilateral treaty environment combined with other OECD strategies is likely to result in different outcomes in the future. However looking back must be done through the lens of what the law and guidelines were at the time. The reality is that taxation law has not and is unlikely to evolve as fast as the ongoing and rapid change in the global business environment.
Both Apple and the EU Commission present their positions in the press with quiet confidence and no doubt there will be many companies awaiting the outcome but it will be quite some time before this issue is resolved.