Despite the pre-order issues with Apple and, my iPhone 6 Plus arrives on Friday and I will be taking a look at it as an enterprise device applied to my professional engineering career.
One area where Apple will be directly targeting the enterprise for those who ordered the higher capacity models is through preinstallation of the iWork and iLife suites. Apple will reportedly include these two suites on the 64GB and 128GB models of iPhone 6 and 6 Plus.
16GB buyers will still be able to, but given that the all the apps take up more than 2GB of storage buyers would likely not appreciate having this much memory taken up by these apps.
The iWork and iLife suites include Numbers, Pages, Keynote, iMovie, iPhoto, and GarageBand. These are not operating system level apps so even though they will be preinstalled you can always uninstall them if you like.
Hopefully this does not open the door for carriers to preinstall their bloatware apps, but if they do then you should be able to remove them just like you can on. This is one area where Android fails, especially if you buy a device from AT&T.