If Apple changed the base model to 32gb then people would just demand an even cheaper 16gb version!
And they'd have that in a $99 iphone6 or 6c or whatever they will do.
The issue is that we are all subsidizing those people who don't want/need more storage. By making an extra $97 or so profit on our upgrade to 64gb, we become far more profitable customers. This allows them to keep selling the base model cheap while making the crazy profit that they expect overall.
Sell the 16gb for $229 and the 64gb for $269. Start sharing the pain if you can't make the profit you want on the base model.
As a consumer, I can buy a 64gb microSD card for $20 at full retail.
Apple can get away with this for only 1 reason... Their app developers.
I switched to an HTC M8 for a few months. The hardware was beautiful. Many people think Apple stole some of HTC's design for the iPhone 6. The screen had a higher pixel density than either new iPhone. It felt every bit as premium as Apple... Maybe more so. It was $69 on contract last year and came with 32gb. I added a 64gb microSD card and had a premium phone with 96gb storage for $100 on contract.
But I switched back because... Apps. And not Apple's stock apps either, as there is almost always a better option. The App Store is Apple's ace in the hole thanks to all of the developers out there. Apple should make it as easy as possible to stuff our devices with those apps and lock us into the ecosystem.
Even Apple Music could use the bump in storage, as I think the everyday customer would be wowed if Apple did a better job communicating that songs can be saved to your device for free. I think the every day customer is more focused on staying under their data limit than using cloud services.