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On a side note why the war against optical media? a BluRay is 50GB of data I know 32GB and 64GB thumb drives are common place now but there is no real reason to eliminate it from a tower.
For several reasons that folks always tip-toe around in these discussions. That it happens to slightly help iTunes sales/rentals is just a "bonus" for Apple.
1. A small contributor is probably Jobs (and NEXT since there are several of them still at Apple) experience with magneto-optical drives on the NeXT cube. It wasn't really the key differentiating factor they hoped it to be. It is "nice" having more storage on a 'walking around' disk, but that gets offset by the limited places can insert the disk to get data back out. In short, if it isn't a rapidly adopted standard, then the utility is limited.
2. Some folks forget now the Blu-Ray HD DVD format war. The fratricide (between optical disks ) war to replace the DVD wasted alot of time and effort. 2002-2008, almost six years is a long time.
It is likely there was a small bet by Apple that the "format war" would inhibit Blu-Ray adoption perhaps to an extent that it would fail to take off. It was inhibited but not completely.
Apple tends to either create their own standards or adopt those of others that are well behaved and beneficial to Apple & users. The transition from CD to DVD went pretty smoothly. The Blu-Ray transition turned back into another squabble VHS vs Beta war. Even if Blu eventually worked these repetitive "format wars" were eventually going to cause lingering problems.
3. Costs. Related to the above but one of the prime motivations for the format war was greed. Licensing fees. java vs. microsoft's firmware. blu lasers vs. higher compression. hd copy protection.
Apple hates other folks DRM. Their own DRM they are tolerant of as a business necessity because need to try to protect the content of the 3rd parties they are trying to derive income from.
But the underlying factor here is that if there is going to be a major war every time an evolutionary step is due to happen then the media is more "drama' than it is worth. For example, due to repressed volumes the price of next generation optical players stayed higher for at least 2 years longer than it should have. That was only going to lead to higher component costs for Apple if they jumped in. If the adoption had been rapid and costs dropped quickly then Apple probably would have jumped on board.
if a ODD costs $40-80 then if dropped then a portion (or all ) of that can go into other components that a broader set of users can leverage ( e.g., more RAM. more HDD/SDD storage. )
4. Blu-ray is 25GB. 50 is only for "dual layer". ( eventual higher capacities was a benefit of going Blue but it took a while for that to appear. )
5. Speed. While USB 3.0 thumb drives aren't cheap yet, they will be much more affordable in the future using a backwards compatible socket. Users can migrate their data to a faster format over time, at their own pace independent of what Apple puts inside the device ( presuming Apple keeps pace with USB socket evolution over time. )
6. Space. For better or worse more "stuff" can be kept in the user's "online" storage device. People don't have to use boxes and cabinets to store tapes/disks/albums etc.
All of those factors don't eliminate the subset of folks using ODD were speed, space, and cost don't matter. However, these factors do reduce the percentage of users using the devices. Once the percentage falls low enough, then it doesn't need to be included for everyone to buy.
For a USB 3.0 or FW ODD an external drive is no slower than an internal one. The format is slow. Other than quirky, limited BIOS boot properties in some situations there is very little that is a unique upside of an internal ODD.