I can't quite follow the issue with the intra-European flights? I generally don't collect on Miles&More, but just out of curiousity: I recently booked a flight from Munich to Copenhagen with booking class K for around 100€. In the old system this will give you you 125 miles, but in the new system it showed me I'd get more than 400, so at least for the cheaper booking classes it sounds like quite a good improvement?