Second, I'm not sure that 25% of the sticker price is an adequate compensation. After all what needs to be done is these cars need to be permanently reprogrammed, and as you say it means power reduction and worse fuel economy. But by how much? It has been a few years now that we (as customers) have to deal with the common industry practice of advertising unrealistic fuel consumption statistics, so I'd say to some extent more car-makers are similarly boned here.
Third, Volkswagen is a group, and owns quite a lot of brands: Audi, Bentley, Bugatti, Lamborghini, Porsche, SEAT, Škoda, Volkswagen, Ducati, MAN, Scania, Neoplan and Volkswagen Commercial Vehicles.
Fourth, it is common that such investigations go on for years without end. Microsoft f.eg. did not pay a single penny for the IE antitrust case.