Even if Apple wins this case, I think this ordeal will put a damper on their security and encryption emphasis.
Imagine being a project manager in charge of a new feature, where the feature could be made very secure and encrypted or not. Imagine trying to justify the decision to make it secure and encrypted to yourself and to your higher up knowing there is a reasonable chance it will bring another legal storm your way.
One of Apple's arguments in this case is that what the FBI wants will have a chilling effect on speech, and the innovation and technology surrounding speech. I say it already has.
Actually, I could see this going the other way. Build it so the user singly owns the data and no one else can get it. This places ownership with the owner. I can see the development of this type of tech accelerating.