The Lightning connector has 8 pins: 2 for power, 2 for ID/control, and 4 for 2 differential lanes of anything. Those 2 differential lines are used for all data transfer, and, IIRC, are bidirectional. So, in theory, the Lightning connector could carry USB 3.0's differential RX/TX lanes no problem.
My guess as to why Apple hasn't implemented that is a lack of demand. Syncing/backup is expected to be handled on the device now, and USB 2.0 gives enough bandwidth for the majority of the other cases. And on iPads where more bandwidth might be required (eg. external data storage), they already have USB-C connectors supporting the higher speeds.
It does seem petty. “I just paid for a $1000 phone with a massive markup and you mean I have to pay an extra $12 to get a decent amount of storage?” It’s not like the 99¢ gets you a terabyte; you only get 50 GB. They could just swallow the cost, but they don’t.
Continuous services are taxed and accounted differently from one-time costs.
They hook you in with the $1 option, you see how useful iCloud is and then you'll fork up even more. Then you notice that your whole family can share the subscription and soon you'll be paying $10 for the 2TB option and are an Apple One subscriber.
That's just good business nowadays. All companies _could_ just sell stuff with an one-time fee and provide a service forever, but it's not fiscally responsible in the long run.
My guess as to why Apple hasn't implemented that is a lack of demand. Syncing/backup is expected to be handled on the device now, and USB 2.0 gives enough bandwidth for the majority of the other cases. And on iPads where more bandwidth might be required (eg. external data storage), they already have USB-C connectors supporting the higher speeds.