Why can't Apple unlock only the phones in question and present them to the FBI?

"Why can't Apple unlock only the phones in question?" Because FBI is not asking to unlock the exact phone. They wish to have a master key which will unlock all the iPhones in the world.

Little background about the scenario : FBI has the iPhone used by the San Bernardino shooter. There is an option to erase all the data in the iPhone after certain number wrong attempts in the lock screen. FBI is not sure whether the shooter has turned on the option or not. They are looking for safe ways to get all the data stored in the iPhone including all his personal data which could be helpful for the investigation.

What Apple has provided so far? : Apple provided all the iCloud data related to that iPhone. The last synced data in iCloud is pretty old. When FBI asked for the new iCloud data, Apple suggested them to connect the iPhone to a WiFi network. So, that the iPhone will sync with the iCloud and then Apple could provide that data. But, FBI couldn't do that since FBI already tried to crack the device and accidentally changed the iCloud account in the iPhone. So, that Apple can't help them with the iCloud data.

What FBI is asking from Apple now? FBI wants Apple to create a specific version of iOS which will disable the existing passcode in the lock screen. Then update the sophisticated version to the iPhone using their DFU mode. FBI claims that this sophisticated version will be used only to unlock San Bernardino shooter's iPhone and then kept safely inside the FBI.

Why Can't Apple do that?

1. FBI is literally asks for a master key to unlock millions the iPhones which are sold till date by Apple. Apple is a user privacy centric company which makes most of its profit from selling the hardware products like iPhones, MacBooks and iPads unlike other giants who makes profit using ads. Obliging FBI's request will send wrong signal to the millions of Apple product users and break the trust Apple developed over a decade which could be capable enough to collapse its entire market share.
2. FBI is arguing that the sophisticated version will be kept safely by them. But, how could Apple get an assurance for that. What if a corrupted FBI officer sells it to any outsider or terrorist group? The whole Apple ecosystem will collapse.
3. Apple currently don't have such version of the iOS. It has to put dedicated workforce and create such version which it doesn't want to develop and which contradicts its own policies. 
4. What if other governments like China, Russia or UK wish to get the copy of the sophisticated version in the future. The risk of Apple's business will be very high, if it occurs. They would quote that you have done for FBI and why not for us.