I don't really get what Apple is trying to achieve with this letter. Looking at my (continental) European colleagues, it comes across as aggressive bullying by a U.S. company and clearly harms public opinion of Apple, which cannot be a good thing for a company that sells consumer products. Maybe it looks differently from the Irish perspective, but obviously Ireland is a tiny market compared to France / Germany / etc., which are all countries where U.S. companies' (legal!) tax maneuvers aren't looked kindly at and where such a letter can only do more harm than good. People don't like the European Commission, but they like "lecturing from the Americans" even less.
In the end, this matter is a very complex legal question (1. were the Irish tax deals actually "deals" or just the day-to-day application of the Irish tax code?; 2. if they were "deals", were they illegal deals under EU rules against state support?). It is going to be answered by the European Court, which I guess (or at least hope) will not make its decision based on an "open letter" posted on the Internet.