Because each storage tier means a price differential and when there’s potentially going to be iPhone SE, 7, 7+, 8, 8+, Xs and Xs+ all on sale, having three price levels makes it harder to separate each device in terms of base cost.
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Serious question - have you ever tried iCloud Photo Library? All of your pictures remain visible as thumbnails in the camera roll, visually no different. The full image is recalled from iCloud when you tap to enlarge. If not accessed again within a certain time it then reverts to the thumbnail on the local storage. In my experience, absolutely seamless and not using it is simply wasting space to cover the very remote possibility of being unable to access a full res image if you’re without a data connection.
Honestly, Apple has shown recently that they don't mind multiple skus, of course a base of 128gb would be ideal, but based on what they've done recently, there's no reason to think they cannot do a 3 tier storage system, 64/256/512.