What Global wrote...
Special Conditions are quite common on new aircraft programs - and the 787 had a bunch due to all the new technology it incorporated (many having to do with the carbon composite construction). New technology can move quite quickly, while new regulations move at a glacial pace (after all, the FAA and EASA are basically just huge bureaucracies). So the FAA uses Special Conditions to address areas where the technology isn't addressed by the existing regulations. Glass cockpits, FADEC, and FBW are just a few areas where Special Conditions have been common. The down side is SC's are a royal PITA to deal with during the cert process.
On the 747-8, I narrowly escaped getting at least two Special Conditions - either by pre-emptively going to the FAA and explaining that we were already going to do what the FAA wanted (uncontrollable high thrust) or by voluntarily stepping up to the newer regulation than what would have been required by the agreed cert basis (HIRF).